What he said, a skill-based system like SWG, and something that simply gives you more options in the field would suit me just fine. A noob - or no, someone who's made a new character, should be able to pop someone who's been playing for a month if he's good. It would ultimately emulate the current play experience, but with a larger goal in mind, as well as the ability to opt in and out (otherwise you would need to be playing 24/7).
Would you have it so that players are more useful to their team than they are for their own merit? Say, a level 60 rifleman emits a small damage aura? And the weapons would likely be "alternative" rather than "superior" a lá Team Fortress 2??
True. It's hard for a rifleman to be a large ship, even though people still float to a degree, filling him with oil or petroleum will make said rifleman non-functional. The term you're looking for is "tank".
I imagine the whole world map would be split up into regions, with key control points/sites that you have to fight for, win and hold. Taking all of these within a region gives you and locks that region. A region can be contested at any time by the enemy attempting to and succeeding to take one of these control points, however the enemy has to be controlling (and not just contesting) an adjacent region. It would still have to be a very much team-oriented game, however NPC's should play quite a large role to populate the place. For example, when you take a control point, it is populated by an NPC army. Additionally, you could log in and if there's no-one around, you could play with a squad of NPC's.
Ehh dont know about MMORTS, id be looking somewhere else for inpsiration prefably within FPS or RTS elemental gameplay... Going MMO would just make Empires into a grindfeast...