This is my first post here, I've been very much enjoying the game so far and this is an interesting thread of suggestions. Mine would be:
1. Increased pool of companions, as mentioned above. I will only play through these games once, and would like to experience each character type. I would love to have a generally good and generally evil companion in each class available. It just feels weird to bring along a load of do-gooders if you want to wreck up the place, and vice versa. Of course, keeping a reasonable level of interaction with each companion would be a real challenge.
2. Improved higher-level magic use in battles, again as mentioned. I find the basic mechanics far more to my liking than those of BG1/2, i.e. hitting, wounding, status effects, utility of all attributes to all characters etc. The one exception is the lack of really cool spells with unusual effects and specific counters. Also, there's nothing wrong with potentially OP effects if they're limited. My fondest memory from BG2 is finishing Firkraag with prismatic spray insta-death: no save-scumming and waiting for a favorable roll, just throwing off a single hit-and-hope and getting lucky, exactly as might happen in a heroic fantasy story!
3. Better ambience. While I prefer the mechanics of PoE, I do think it has yet to match the older games for atmosphere and immersion. On that note I personally found the golden-named backer designed characters a massive turnoff: their individual stories were fine, sure, but I feel they came at the expense of characters who could actually have fitted into their locale and built up atmosphere, rather than had individual "cool stories" that sometimes barely seemed to make sense in the setting of PoE.
I'm excited to think that if Obsidian improve a few small things, PoE2 could be right up there with BG2/ToB!