Thumbs down to ship customization! lol. Just a personal preference. Starfleet isn't Johnny Freelancer wheeling around the universe in his custom cargo cruiser with all sorts of parts and pieces rigged together, you know.
More on the subject, I'd love to see a Trek MMO that was territory based. You fly missions and whatnot, but every planet or whatever has a allegiance level, so territory can change. I don't care for MMO's where you take over an enemy town, but the NPC keep respawning unfriendly. At some point the unfriendlies just arne't going to be there in meaningful numbers and friendly NPC's should spawn, right? Sure, this could mean that some race may get wiped off the board (or a least mostly) but there is always a chance for a comeback, especially if they have crafty admins helping to shape the storylines, without looking too much like they are trying to keep one race from being wiped completely off the board.
I would like to see more than just combat missions, however. Missions of mercy, to help colonists, and whatever, for those who aren't interested in war (I'm assuming all those players will be Fed
).
I actually like the concept behind STO where each player has a job to do on the ship and in order to do combat, you have to have all the stations manned. But, the lack of meaningful pvp (holodeck only? What's that?) is a major let down. Then the whole instance thing/undefeatable, unseeable rookie ships idea really leaves me wanting. Anyway... I'd probably give something like SFC a go if it were an mmo, but it would have to have the combat depth and leave out ship customization ala SFC3.