If possible design more detailed and dramatic deaths, similar to how programs die in the new tron movie. Also i think music along the lines of what is already in the game but more "energetic" would make it more enjoyable. I dunno if you can legally use tron music from the new tron movie but that would pwn.
Assaulting cities and fighting navies would be awesome. Also, instead of buying upgrades why not instead have research, and the player has to hold out while research gets completed?
yes... let the want flow through you.