Add real music to the game. It is essential to hear different tunes that convey different things to get the mood of the level your playing. The desolute sounds work okay for some of the desert levels, but we need some adventure tunes for forest levels, and some haunted music for ghost populated levels etc.
The next thing that is essential is to show what kind of weapon you are carrying! It doesn't have to be a different animation for a bronze sword and a shaped sword but heres what I want. An animation for carrying a daggar, carrying a baton, carrying a sword, and carrying a wand. Its annoying to see my character lift up a sword when he is casting a spell with a wand. For serviles, enemies and non enemies, this would be a good idea to make them all look a little different.
Finnally balance changes! Instead of making a it a race to the uber creatures, make some of the lesser ones be more specialized (poison attacks or haste special etc., and make more of them so its a good comination to have one heavy hitter (like an eye beast) and a few weaker ones. Also tone down the eye beast a little by making his attack weaker against you if your armor is high. And tone up the guardian drakon, hes not worth the cost.
Also make it so you can use the Geneforge, lots of people want to use it so they can make tons of creatures, even if it ruins the ending.
The kind of plot I want to see for Geneforge 3 is where something terrible has happend and the shapers and serviles have to stop fighting to destroy it. A huge event, like demons or something. Also make this take place in the Shapers world!!! No one wants any more colony adventures!
Another great thing would be some multiplayer support. Alot of my friends have geneforge 2 and we often compare stats and items that we have. Being able to have a 1v1 battle against a friend would be really fun. It would be just like any other battle, just on a newwork.