I was thinking of what I would like for TU2's free-play mode, and first off I think it's really necessary to be able to play skirmishes in any the game types that were in TU1 and any new ones that will be in TU2 (hub, hub/network, seige, etc..).
Second, I was thinking you could add a conquest mode that looks something like the level map you posted on Sept. 7 only perhaps more of a square, since the sectors you see in the sky are square. I think this could increase play time quite a bit.
Then I thought, "why not multiple sectors?". Basically that could work by having blue start with one (the one from the story? or maybe this could be just generic "blue vs. red", to keep things simple) red start with a couple, maybe some uncontrolled or virus. I was thinking you would build cap ships (e.g. the Revelation) or smaller landing craft to invade other sectors. You could then (using your "user powers") go from front to front and fight the different battles in different sectors.
A downside of this would be that it adds a lot of strategy (which many people seem to want to avoid) and could potentially get boring, seeing as how long a single battle can take. However, the main opposition you express is that it makes the battles to complex, but this wouldn't really change that. If this is too much for one game, it could be something like the Mechwarrior series, where they made Mech Commander as an RTS to supplement their previous FPS's, but I think at least single-sector would be a good idea, since you're already considering doing that for the story.
Also, I know you are hard-pressed for time and couldn't devote too much to this, but I would be more than happy to help develop the idea.
I could go on longer but I just wanted to give you a good idea of what I was thinking. love the game, btw - looking forward to TU2.

