I have a few ideas, some which may have been expressed before, I haven't read through all the posts.
1. A replay function. I think that you should be able to watch what the A.I. does in order to see how they beat you. For instnace, after the game you think, why didn't the Yor attack me? When you watch the replay you see that they were fighting the Drengin and losing.
2. A save function of starship designs + basic designs. Not everybody wants to choose exactly what modules to put on a starship. Some might just want to use say a basic transport without having to indiviually load up all the modules and put on engines and all that. Others might want to save their mega ship of DOOM!
3. Simply building a military building should train all the militia neccesary for that building. You should not have to indivually train each soldier. Same goes for transports.
4. Artificial constructs of large size should be included, like a small artifical moon that is something like 2 x 2.
5. All tiles should be terraformable with the right technology no matter what. If you can travel the stars you can level a mountain I'm assuming.
6. Race specific upgrades. Upgrades to certain tiles that increase production and each race gets a different effect. For a custom race, there could be a list of possible upgrades. For example, the drengin could get a slave factory, that increase output on a farm. (Slaves can be food)
Well thats it.