Gonna make a bit of a rundown here as to my thoughts about how likely it is to see each companion from the past games to return for the next one, based on my expectations of what a third Pillars would be tackling in terms of conflict and themes. So basically with Deadfire we're left with a major conflict at hand which is the Wheel having literally been destroyed, and kith and gods alike needing to figure out a way to rebuild it so that souls can once again pass to their next lives and so on so forth. Naturally I'd expect the third game to deal with this conflict... But from a thematic standpoint also deal with the relationship between gods and men, of the move towards a more secular and humanist society as the past connection between the aforementioned two is reexamined and reevaluated, or maybe even restated depending on the Watcher's choices leading into the creation of this new "Wheel" and so on. So, if so I expect more involvement with gods, more debates about religion, animancy and general existentialist stuff, more Watcher shenanigans and so on (though it may well be me expecting what I'd *want* to see instead, as it is what I love most about this saga... But I digress).
So, with this in mind, here's the list of companions ranked from most to least likely as far as I see it, with an explanation for each...
(As a small caveat I'll mention that I haven't played any of the DLCs for Deadfire yet, so I don't know Vatnir at all nor have I seen any of the new stuff for the other sidekicks and so on)
- Eder: He's the franchise's mascot, for better or worse, and I cannot imagine him *not* being in another game involving the Watcher. Initially I reckoned he'd have a little more at stake with the conflict of Deadfire given it's *Eothas* of all beings that we're chasing, but that was rather underused or underdeveloped... So I don't exactly see a thematic link with this third part beyond general Eothasian beliefs/faith keeping him doing what was Eothas' will, and maybe the fact that he is one of those few who knows straight from the horse's mouth what the gods truly are. Same could be said about any of the other companions, but he seemed especially affected by the revelation.
- Aloth: Semi-mascot status, I suppose. As a character that holds a deep relationship with the Leaden Key either way, he seems rather primed to have an investment in the events that would potentially change the relationship between gods and kith forever. The Leaden Key for one would definitely have an interest in influencing that process in some form or other. Besides, whether or not he continues his work dismantling/reforming the cult at the end of Deadfire, it still leaves him in a perfect position to pop up elsewhere in the world *or* follow the Watcher in a new adventure that may also further whatever goals he now has.
- Ydwin: Ever since she was announced as a potential eighth companion she's grown to be something of a fan favourite, and given that she never quite received a full companion treatment the devs could maybe fulfill that part by her inclusion in the next game. Regardless, her conflict, her interests and her profession seem especially poignant for what is going on currently in Eora. Already before Eothas did His part bringing down the Wheel, she'd found a way to remove herself of it, and this places her as both a character far more aware of the inner workings of the Wheel and reincarnation system than any of the other companions thus far, and with a pretty singular stance on the matter too. Much like Pallegina, Maia, Serafen and Tekehu were the voices of their respective factions in Deadfire she could be something of a voice for animancy or the more secular side of the argument going into the third game... Or maybe just another view within several relating to this matter.
- Kana: There's a pretty massive gulf between the top three, who I think are all likely or at least possible, and the rest of these who I feel are more likely *not* to appear instead. Of these I'm not sure why Kana's the most likely, but I reckon it's because he's the one with the greatest combination of autonomy and motivation to join the Watcher in a new adventure if it should so happen. As a student of lore he's likely to want to observe and record this particular historical event from as close as he possibly can, and how better than with the figure seemingly at the centre of this conflict? Add to this that he's something of a fan favorite too.
- Xoti: Xoti's motivations to follow the Watcher are somewhat similar to Edér's - potentially strong relationship with the Watcher (especially if they are lovers and so on), a follower of Eothas doing the last of Eothas' will, decent autonomy and so on. She could possibly take a stance rather opposite to Ydwin's own, or maybe a more positive take on the influence of religion and the freedom of belief following Eothas' own desires for kith, whilst opposing another more dogmatic or gods-fearing character and so on. My concerns about her are whether we *need* two representatives of Eothas in the first place, and whether she is liked enough by the community or is interesting enough as a character to justify a return (granted, this last bit can be applicable to Kana too).
- Rekke: Again, people have seemed to taken pretty closely to Rekke, and the fact that he's basically learning of the rest of Eora from the Watcher's hand places him a little closer to his adventures than the likes of other sidekicks, who as fun as they are don't really have much of a motivation to follow the Watcher around. But this would also assume Rekke was taken in as a sidekick and the Watcher actually took time to talk and explore Rekke's past and whatnot - which could well not be the case, and then he'd have little reason to be attached to the Watcher in the first place. Rekke's own relevance to the conflict I outlined before is negligible too, I feel, which doesn't help matters. I can actually see a scenario where he comes back as an NPC of sorts in whatever stronghold we set up this time around than an actual companion, kind of how the OP was suggesting.
- Hiravias: Plenty of autonomy and a connection with the overarching themes of the Pillars franchise given his faith for Wael and the way in which in the first game he was something of a voice for the debate about the *logic* of men opposed to the logic of gods and so on. Maybe his part of the dicussion is done at this point, but regardless I always found his character to have some of the most interesting and perspicacious takes in all matters religious in the first game and, indeed, the saga as a whole. On the other hand he doesn't seem someone who is awfully concerned with the "current affairs of Eora" and seems to only join you the first time around on something of a whim which happens to be convenient to him in the long run. He could appear but I don't feel like he'd have a specific motivation to be wherever the game takes place in or to actively seek out the Watcher for that matter.
- Pallegina: Dunno what to make of her really. She was something of a fan favorite in the first game and people looked forward to seeing (and romancing, RIP) her in Deadfire, but I for one was quite lukewarm about her treatment in the sequel and haven't seen much love elsewhere either. Regardless, by the end of Deadfire she's either pardoned by the Ducs and reinstated into the Brotherhood, or banished forever, and all that leads after seems very final and I just don't see why she'd have any reason to return, or any motivations that wouldn't simply feel tacked on. As a godlike and a hard atheist she could have some investment in the conflict in that regard, but nothing unique enough to justify her specific presence the way it would Ydwin, for example.
- Tekehu: He's great, but again, I don't see much reason or personal motivation for him to be in a sequel or to really leave the Deadfire Archipelago anyways. It feels like his story, and his part within the Watcher's story, is done.
- Maia: Maia was a mistake. Far as I'm concerned, nothing gelled about her character whatsoever, her "arc", such as there was one, went nowhere, her views seemed contradictory, she seemed to exist in Deadfire to be a voice for Rauatai and little else. Unless the followup happens in Rauatai itself I don't see her making an appearance, and even if it does I don't see why we wouldn't be better off having Kana instead.
- Serafen: Great, hugely likable character, but already in Deadfire his relationship to the story and conflict felt tangential at best, and was likely the loosest faction representative we had too. His character arc was satisfying within its own little microcosm but it's not something that seemed terribly interesting or relevant in the greater scheme of things, the way some others were. Much like Hiravias I also feel like he didn't have much of a personal motivation for following the Watcher in the first place (opposite to Hiravias, he was kind of forced into it), and by the end of the game he doesn't seem to have any real motivations to leave the Deadfire or the pirate's life. All in all I'm glad we had him in Deadfire but I don't see him returning nor would I miss him in a sequel either.
- Mirke/Fassina/Konstanten: I have very little to say about all these because I didn't invest much time with them. Based on my limited experience with them, they're all colourful enough characters with enough autonomy to follow the Watcher in a new adventure if they so wished, but with no real hook to do so off the top of my head beyond a mere "they tagged along". So, in theory there's nothing preventing them from returning, I just don't see why the devs would bother.
- Sagani: Like Pallegina, her arc is done. Unless the third game involved Naasitaq in some fashion I see absolutely no reason for Sagani to return.
- Maneha/Zahua: Grouping these two because the reasoning is pretty similar as the above - basically their arcs are done. And they don't even have a setting to justify their return either.
- Durance: Ignoring the obvious reason that the character was created and written by Avellone, if I'm not mistaken Eld Engrim also suggests early on that Durance died by the time of Deadfire's events. It's a shame as no doubt he was one of the richest characters in the first game in terms of both lore and relationship to the story/themes that still drive the saga to this point, but for what it's worth his arc was also pretty concluded by that point.
- The Grieving Mother: Everything I wrote about Durance applies to the Grieving Mother too, only that I feel her existence was way more self-contained and her arc was also given a much clearer conclusion than Durance's. If Avellone was still around I could have seen a potential return of Durance in a sequel, but never of the Grieving Mother.
- The Devil of Caroc: She's dead, Jim. At least she made for a good breastplate.
I've kind of read through most of this and skimmed the rest. I don't know that I entirely agree with your conclusions, but it's great that you put this much thought into it.
One side note before I get going. I always assume that Eder and Aloth come as a package, since they use the same voice actor. Hey, it's not an absolute lock that both would be in a PoE3 if one was, but it does seem at least somewhat likely that if you had one, you'd have both. Anyways, moving on...
Eder: He seems to be the Watcher's best buddy who will always have his/her back. Not a guarantee that he'd be in a PoE3, but that seems to make it more likely than the other NPCs (using NPC rather than trying to constantly type out Companion and Sidekicks).
Aloth: Personally, I wish that Aloth would go away. I've never warmed up to him. About the best part of Aloth is the interactions with his secondary personality. And that's not a lot to hang one's hat on, so to speak.
Rekke: I think that it would depend on what the story of a PoE3 was. If the PoE3 story was to take Rekke back to Rekke-land, then it seems rather likely that Rekke might be a full on Companion. OTOH, if the PoE3 story remained in the known part of Eora, Rekke might be history.
Ydwin: I don't know if there's anything tying her to the Watcher. That said, I think that she's an interesting character and it'd be nice if she stayed with the Watcher. Heck, it might even be interesting if the devs let Eder and Aloth go their own way, and pick a couple of different NPCs to be the Watcher's best buds. And I'd suggest Ydwin fill Aloth's slot as a spellcasting buddy. And then pick someone else to be the physical combatant pal.
Kana: I agree that there really should be a strong tie between him and the Watcher, largely based on Kana's love of lore and wanting to see what the Watcher does next, since "you" seem to be at the heart of so many major events that affect Eora.
Konstantin: Nothing about him interests me. Maybe it's because I like characters who fit the stereotype of their fantasy race, but I'd rather have a Mountain Dwarf who was a fighter, priest, or the combo of the 2.
Mirke: I don't mind her as the perpetually drunk pirate girl, but I do not like her as a monk. It just seems so damned wrong. From my perspective, she should have been a pure rogue, a swashbuckler, or possibly a rogue/chanter (or fighter/chanter). To me, monks should be characters with a lot of discipline, and Mirke is exactly the opposite of that. And honestly, I don't really see her as the sort of character I'd want around for PoE3.
Maia: The devs obviously needed a companion to be the RDC's voice with the Watcher. And maybe they didn't feel that a Chanter (i.e. Kana) was a good fit for this role. Maybe they saw the character who would fill the role as being some sort of soldier, and it just progressed from there. Or maybe it was as simple as the voice actor who played Kana in PoE1 wasn't available for PoE2.
Xoti: Nothing really against her, but I'd rather see a different priest companion. (Perhaps, it could be the Mountain Dwarf idea I mention above...)
Fassina/Vatnir: Neither of these two strike me as adventurers at all. Fassina's "paper doll" figure on her inventory page show me a character who looks like I should have left her back in Arkymr's magic shop. And Vatnir strikes me as too much of a coward to be the sort of adventurer a veteran Watcher would want to have at his/her side full time.
Pallegina: I like Pallegina and love her accent, but I think that it's time to move on.
As for the others I haven't mentioned, I pretty much agree with you. Besides, there really should be some turnover in the playable NPCs just to keep things fresh.
One idea for a character that could be interesting comes from Beast of Winter. Remember that pale elven warrior whose soul you met in Rynrgand's realm? The one with the somewhat flat, emotionless voice with a hint of an exotic accent. Now that character's dead, but I'm think that a character based on sort of the same idea. A ale elven female fighter or paladin who had a similar accent (perhaps even the same voice actress) might be really interesting, particularly if she had a bit of a snarky "straight man" attitude. Sort of the way that Spock in the original series could be really snarky (particularly to McCoy) in spite of his Vulcan emotionless. The one downside of this character being a pale elf would be if Ydwin was still around. It might be better if this character was either a wood elf, or could be a pale elf if Ydwin wasn't one of the playable NPCs. Come to think of it, this character wouldn't even need to be a fighter or paladin. I could see her as a wizard or a ranger too. Probably not a chanter or a barbarian. Maybe a monk. Probably not a cipher, if only because why bother creating another pale elf cipher when you have Ydwin. I guess what it comes down to is that I really loved that Beast of Winter NPC's voice, and would love to have it used in a Companion if there was a PoE3.
Anyways, those are my thoughts...