I enjoy the game as it is, and a lot of things that I'd enjoy have already been suggested. (More species models/better models, make maybe FP better, more variety in maps, etc.)
However, one thing I'd love to see would be a better way of making presets. As of now, creating a preset is much like retexturing models. And it's surprisingly difficult to get things lined up once. A long time ago, I saw that someone was going to be making a little program type thing where you had the model in front of you in 3d and coloured on it. This is very similar to how custom MineCraft skins are often made-- you see the model in 3D in front of you, and how it lines up. I imagine it would work similarly to an art program with select turned on: You have the other textures for the other body parts on, and colour on another. It would make the difficult task of lining up scars and other markings far, far easier, so you can spend more time on actually making the textures and the code.
I know incorporating the glow, transparent, and other preset codes would be a dream come true, but I know that it's impossible.
A similar thing or the same thing for map height and terrain maps would be even more of a dream come true, but it might also be kind of difficult.