Some of my thoughts on the subject:
1) A lot of people seem to have a problem with the appearance of their character. Why not dissociate the type of character from their appearance. There would still be guardians, shapers and agent, but your agent could look like a shaper (or the opposite, if you like the swimming suit of the agent better ). In the endings you always look like a shaper anyway.
2) I like to play with "free creations", it makes me feel less alone. It would be nice if their AI was making them follow you, instead of fighting every enemy in sight. It would make it a lot easier to keep them alive, I am so sad when one of my friend dies, I miss the friendly rat a lot )
3) I agree with the limit of two skill points from a trainer, but the quest rewards, books and perhaps even canisters should not be taken in account for that. I know it has already been told, but I find it really important. When I reached Learned Guas in outer Gazak-Uss, I found out I could only buy him battle and mental magic (I'm playing as a guardian )
4) Talking about money, trainers and also nice equipment, they should be available sooner in the game. I understand you have to deserve them, but if you get the best armor in the game by killing the last living thing in the game, what's the point ? About money, I needed a lot in GF1 to buy luck and mechanics, and I spent a lot of time selling things like thorns, javelins, robes... because I wanted those skills as early as possible (when they still make sense) and at the end of the game, I was not even taking the money from the guys I killed...
5) About the last two areas in the games ( crypts in GF1 and Gazak-Uss in GF2), I don't really see the point of them, except for having a good fight of course well, if you like it... In GF1, I went in the inner crypt and had Danette'belt before dealing with Trajkov and Goettsh, so it helped a little, but was really unnecessary. In GF2, I already finished the game with different endings, but I've not explored Inner Gazak-Uss yet. And I don't really want to do it because I hate eyebeasts and there would be no change in the endings (that I know of). It would be nice if those areas had something interesting (but not really necessary) for the endings (as there is nothing else left in the game at that point).
6) I agree with Shellbullet about the conversational or diplomatical part of the game. You should be able to share your opinion and perhaps influence some characters with enough leadership. For exemple, if you are allied with the Awakened, you should be able to convince some other serviles of their rights and make them join the Awakened.
7) For the easy and perhaps normal mode players (that's what I am ), be careful with the damage done by the enemies. Some things are really too difficult to beat compared to others. I really don't like the acid or flaming bushes (especially when you play with free creations), and eyebeasts are just too strong (a lot of damage, multiple damage + dramatic decrease of your AP ) Some players may become completely mad, perhaps I am already
That's all for now. I hope some of my ideas are not too bad...