Half the problem with the plot holes is that the writers - deliberately, at least in some cases - left a lot to be read between the lines. The other half of the problem is that you really need to work to get the information. I think that, in the end, it is less a matter that the ideas were underdeveloped than that you do not need to read half of the plot to play through the game.
(No real point in spoiler warnings for this thread, right?)
G0-T0, for instance will not really talk to you unless you successfully examined the pazaak droid, the swoop droid, did the Bith scientist quest, talked to the droid in the hidden room in Vogga's droid warehouse, *and* had the discussion thread about why you cannot bring droids into the Jekk-Jekk Tarr...
Once you do, you find out that he is a Republic droid. And yes, his backstory fits with the betrayal theme that shows up everywhere else.
Basically, all the characters are like that, and if you have not explored at least a few of their dialogue threads in depth, trying to figure out the ending is like working a diagramless without all the clues.
To start with - here's what I *don't* know: Canderous, HK-47, and Hannharr definitely have more to say, but I have not gotten them to open up yet. The rest, well... I *think* I learned what there was to learn, but I may have missed a trick or two. Any notes on how to get them to open up more fully would be most appreciated.
Beginning at the beginning -
The Exile ended the Mandalore wars by using a mass-shadow device (some kind of gravity bomb; perhaps a precursor to the Imperial Interdictors?) on Malachor V. That is the initial sound, and almost everything in the game can be understood as an echo of that event. The intensity of the event also led the Exile to completely sever his or her connection with the force, something (to everyone's knowledge then, at least) never before done. The Exile must seem undead to Force users, and if the Jedi are right about the Force being the flow of life, perhaps the Exile is. These two things - the role of the Exile in bringing about just about everything in the KOTOR II present day, and his or her unique freedom from the Force, are what interests Kreia. Remember Kreia's point about planetary manipulation on Nar Shadaa? The Exile is her choice of critical point.
Darth Nihilis? Pretty clearly learned his life-eating technique from the Exile (observation, not instruction); his choice of ship also indicates that he was at Malachor V. In the years since, he has refined the technique until he is more hunger than man - the darkness in which all life dies, if I do not misremember Visas Marr. He is extraordinarily dangerous to everyone... except the Exile. After the Exile injures him, he dispenses with playing around and tries to devour the soul, or life force, or just plain Force of his opponent. And it does not work, because the Exile is outside the Force, only accessing it indirectly through Kreia and company. This leaves Nihilis just starving himself to death faster - no wonder he goes down quickly. It is strongly implied that he might have had problems even if he had not faced the Exile at Telos - the discussion with Visas Marr implies that Kreia manipulated Nihilis into going there although there was no Jedi Academy, and that therefore Nihilis would go hungry. Presumably, this means that he gets hungrier when he acts than if he waits, and fighting a Jedi duel must involve a fair amount of exercise. He had the (twisted) Force equivalent of blood-sugar crash.
I must disagree that his sole or greatest significance is that he can defeat Kreia, true though it is and important as that is in understanding Kreia's plotting. He is also there to show the Exile what the Exile might become. He is yet another echo of the 'wound in the Force'.
Darth Sion? Kreia's apprentice who never got over her. Earlier comments about this in the thread about him marking her but not killing her were very well taken - I will edit in appropriate credit when the search function works again for me. [edit - Maria Caliban, post 55]
I see several complaints about G0-T0 and Bao-Dur's droid, both the Ebon Hawk cutscene and at the end. Others have addressed this before, but it keeps coming up, so: G0-T0 does not destroy the droid, he incapacitates it. There's a shower of sparks and it drops to the ground - it does NOT explode. G0-T0 does this to reprogram the droid, with the results seen later. Again as earlier posted [same note about credit where due when I can search| edit Junior, post 62] G0-T0 is perfectly willing to blow up the planet if the Exile so orders, believing that the Exile in making that decision either way will establish a stable religion for this section of the galaxy. His interest is not blowing it up too soon if at all, because Bao-Dur wants it blown up regardless in order to expiate his guilt in creating the mass-shadow device.
What comes next? There are so many hints about an empire of True Sith out there that this seems the obvious course.
What came before? I wish I knew better; DarthPanda's reconstruction of how HK-47, T3, Kreia, HK-50, and the Exile ended up on the Ebon Hawk sounds good to me. I will go one step further and say that Kreia knows more about that empire - or whatever it is that Revan went after - than she let on. I suspect that she saw Revan there, or at least picked up the Ebon Hawk there, and returned seeking to destroy the force so that she (and everyone else, not that she cared) could find her own destiny.
Questions that remain - the HK-50s. Sure, G0-T0 says he purchased the loyalty of several - but not *all* of them, and there's a factory out there. Who's running it? It's not G0-T0 - he discovered what they were up to, and then exploited the information, but he didn't program the 'wanton slaughter' into them. Also, G0-T0 implies that HK-50 core programming involved getting the exile, contracts aside. Obvious candidates are Czerka (a Czerka executive built HK-47, as I recall) or HK-47's last(?) master Revan, or maybe even someone higher than G0-T0 in the Exchange. I do hope that HK-47's dialogue settles some of these things for me, some of his early comments about the use of the sonic sensor imply that it can be done.
One thing that I think we have mostly missed is the power of negative influence. The designers repeatedly stated that both high and low influence have their uses, and given that influence and alignment correlate positively, my bet is that you can train people to be Jedi just as well with low influence. They may hate you, but that just means that you have a party member with access to the other side's Force powers on the cheap. Possibly, they actually betray you - I do not know of anyone who has spent a full game angering their party as much as possible, or even specific individuals within the party, Kreia aside.
Side-notes: the Sith ritual is pretty clearly about controlling the beasts to attack the Queen. The comments made by the final opponents in Freedon's tomb are about how they just need to keep it going, and how it is too late to stop them fit perfectly with the giant beast assaulting the forcefield, and then turning on everyone.
The constant stream of Sith Lords/Marauders/Assassins at the end, although irritating as gameplay, makes plot sense. It isn't that somehow Kreia or Sion gathered more Force-sensitives than the galaxy had seen in millenia in one place, and trained them to mastery - they are just reflections. They are ordinary, perhaps slightly Force-sensitive people who learned the art of feeding off the Force as Kreia explained early on. They were weak then because the Exile was weak then; by Malachor V the Exile is a major player, and therefore so are they. If you assume that they tap into their target's Force channel - and you are drawing on the Force, even if indirectly - while Nihilis draws on his target's life through its inevitable connection to the force (absent in the case of the Exile), then their ability to do so makes sense despite Nihilis' incapacity. That may be stretching things, though.
Why do the Sith matter to anyone but the hunted Jedi? What do informed people think the Sith will do when they decide they have caught the last Jedi? Right, come out and start in on the less Force-Sensitive population.
Is the Malachor academy ancient? I had rather gotten the impression that it was new - founded by Revan for his conversion purposes, and then appropriated by Treia and co.
The Mira/Hanharr confrontation - maybe Kreia's twisted little gift to your apprentice, in hopes of making her stronger? Something she saw in the force? A way to set up Mira for her own spin-off?
Things I would really like to know - low influence results for all, HK-47 full influence, Mandalore full influence, Hanharr full influence, if anyone had a payoff for convincing Viklu's subordinate to help blow up Nihilis' ship, if anyone could cleanse the areas of dark energy at Freedon Nadd's tomb.
Stinger - Who else _loved_ Kreia's response to a Light Side attempt to redeem her at the end? I found that a perfect capstone to a great (although, as she admits) not very charismatic character.