I know I wouldn't want the skill tree system like in Avadon and the new Avernum. I like the customization possibilities of the "old" skill system and frankly few games offer that these days.
What I would like to see is some more skills added, perhaps a general "shaping" skill, or "anatomy", "riposte", or "bartering". I guess either an expanded general skills category or a new one entirely.
That brings me to the next point; guardian specific abilities. The agent has her magic and the shaper his creations, but the guardian doesn't have his own cool thing. There are no disciplines like in Avernum, and that feels lacking.
Another thing I'd love to see is some way to get extra inventory space. Whether that be a junk bag, pack ornks or creation inventory, this would be a wonderful thing. Trudging back and forth five times to sell all that loot is not a pleasant part of an otherwise wonderful game.
The second last feature I'll mention is for the NPCs who join the party to have armor and weapons, and maybe/i basic skills trainable (like giving Greta + 1 to spellcasting).
And for the end; for creations to earn xp based on the level of the creation, not the PC. This is somewhat of an irritant midway through playing, especially in G3 (for me at least).
To sum it up: no skill tree, more skills, battle disciplines or similar stuff, extra inventory, more customizable party NPCs and creations getting xp separately from the player.
I know these things can be difficult and ultimately Jeff decides on what to add so I really don't expect all of that. Any one thing would be nice.