Fyron:
http://www.stardock.com/media/twilight/index.8.jpg
In all honesty, i still love MoO3. I liked how each planet had a biosphere with temperature, atmosphere, heat, surface type etc. All modifying the ability of your race to colonize and develope the world.
I really like space combat as well. Forming squads of ships which will fire their stuff. And orbital bases...that was awesome.
Ground Combat was likely the best model i have seen at this point. There is no way you can compare it to SE, Baron.
Each species had several distinct abilites for fighting better/weaker on underground, air, surface etc. Plus their were like 20 abilites (strength, endurance, to-hit, lifepoint etc etc). In addition, there were 7-8 different troop types, (milita, marines, headquarters, agents, tank, battleoids etc) all boosting different aspect and all more or less suited for different terrain.
In addition, attacker and defender could each select one of about 20-25 different tactics (prone, sweep, fall back, full-assault etc etc) which had different combat power modifiers depending on the combination of attacker/defender tactic. And when winning a ground combat you gradually conquered regions of the planet. And you could place military DEAs on a planet and they would work like military bases, holding the invasion for at least one turn per military DEA.
MoO3 was so bugged, but awesome. It still is my favourite 4/5X game. I can only assume its full potential.