I'm going on the assumption that it's being considered whether or not you guys will do an enhanced edition, personally I hope you do.
What I would like to see:
-An improved tag system, that is stuff like the Spider Kiss talent becoming a tag (rather than what it currently is), and having more general benefits. I've only had one encounter so far where it applies (speaking to Skitters, the friendly attic spider (their name is not actually skitters)), but I think it would be better served in another way. You could create a new skill(s) that are limited only to this tag, which would be granted over a mini-questline of their own (seek out the approval of the Spider Matriarchs), each one would unlock a new special skill that would demonstrate your progression down the path, perhaps with changes that are more permanent (in general), in the case of the spiders you might gain the webbing option permanently, become immune to webs, gain a new venom option, and new talking options with various spider creatures. We could gain something similar in the form of other werecreatures like werewolves, or progress down the path of undeath (as a living creature). As an undead progressing down the path of undeath would be the only option, though as a reward you'd gain access to an even more powerful ability (like becoming a Lich). It would add something a bit more thematic to the game in terms of 'searching for power through less than scrupulous means', and would add replayability (the unique new abilities, dialogue options, etc.).
-Improved items/quests as needed, I've noted before that there are times in which items were clearly overlooked, rings that say they grant chameleon in the description (but don't), 'evil' swords that are white-quality w/o anything but the initial accompanying dialogue, and no development beyond that, etc.
-Rework Polymorph so that it's less centered around a primary summon, keep the primary summon, remove the totems, replace the totems with AI-summons that are specific to spells (Summon spiders, wolves, etc.), which have specific reasons for summoning them (applies atrophy, slowed, knockdown, bleeding, etc.). This keeps the pace up, so that we're not cycling through a bazillion controlled characters, and aren't so overbearing that they are ridiculously over powered. Allow up to two summons for the group at a time. Give the empowering abilities a secondary-effect in the form of direct stats (strength), per bolster they gain more power. Make each bolster cost 2 action points, (for a regular limit of two per turn), giving like 2 strength, constitution, intelligence each bolster. This will naturally limit the number of Incarnates up at a time, by simply limiting how much power you can pump into one (the attributes increasing value should scale, so that they stay competitive, and should scale with summoner level, so high summoning gives a far better improvement). Significantly nerf the base incarnate without empowerments so that it is reliant on these point dumps to gain power, and maybe grant it a unique ability at each threshold.
-Redo the whole 'hunt down these guys to gain more maximum source', instead make it so that each master increases your point total (like it is currently to max 3), but also that they have a unique source skill that you can receive from them (encouraging people to seek them out).
-Increase the maximum skill level from 10 to 20, it seems kinda odd that it was limited to 10 for investments.
I might add more later, I'm only 40 hours into the game this playthrough, might see more or think of more.