Couple of random thoughts
Z axis should be removed from the game (not scrolling into and out of planets, but controlling fleet to move in z axis should be removed).
Research labs could be play a more interesting role in the game than they currently do. If they get destroyed, then you should lose ALL research (including HP, etc) until it they are rebuilt again, not just a select few researched things like units or ability for cannons to fire etc. I mean, it doesn't make sense that, for example, units should still have higher than baseline HP or shields without a single research lab..Just my idea. I guess the exception could be ability to colonise volcs or ices.