Well realistically with hacking up code and touching the code much we can:
Do high res textures(for the aliens I'd blow them up and brush in more detail using Blender's texture painting),
I've tried but Trem rejects them have an idea why!?!?!?!?
More and better animations since they aren't good. I can animate(I'm amateur but I can!), but will have no part in trying to get them into trem as it sounds like a hair ripping mess.
New 1K poly count Building Models(for the people who have slow computers they can stick with the old ones!), should be very easy modeling(honestly first19 could, I can etc) them. However it will "interesting" on how to get the models, animations and textures all into trem. I can easily model and texture, and animate the buildings. But won't rip my hair out to get them in.
Possibly(involves coding) there is a way on the mapper side of things to get better light map baking because the current one on max quality is a complete joke.
Maybe crank up or redo the partial effects for more particles, higher res textures for the particles and such.
Shouldn't be terribly hard, but you need to mess with the code to control the emissions and reaction of the particles.
Multilayer textures because nobody uses them, well not much anyways.
That's all I can get off the top of my head