Alright. If I could, I would make a sci-fi MMO with the following:
I would make a game that really tries to give a satisfying teamplay experience. A focused game that isn't afraid of being unappealing to solo players. That gives it a lot more freedom to make the teamplay part BETTER than other games. Gameplay should revolve around small groups of players working as a team, with the game guiding them towards common objectives. The goal is to make the player feel like an integral part of his team by designing combat around specialized roles (but not the usual dps/tank/healer trinity. More roles, especially different roles than what we're used to see. A sci-fi setting has lots of room for new roles). Great care should be taken to streamline the teamplay experience basically - I personally think that modern MMO's do a surprisingly bad job at this (healing = staring at bars and other such sins).
On a larger scale, the game type would be faction vs faction vs faction. Two factions is too static, three is dynamic and leaves room for self-regulation. Outdoor zones plus instanced areas.
I would also take great care to give sandbox elements their firm place in the game. They empower the player and everybody wants to express himself in the game in some way. Let players build and combine things in whatever way they wish. In a sci-fi setting, modular ships similar to EVE online's T3 ships are a nice idea. At the very top there should modular stations and carrier ships that players can aspire to build, or destroy. Their number should be artificially limited to make sure they stay special and to avoid the endgame becoming all about getting more stations or carriers (or similar economical arms races).
The skill system should be fluid and open. Players gain skillpoints and can spend them on skills. There is a limit to how many skills a player can have. The skills broadly define the role of the player. Skills can be gradually re-assigned over time. Equipment narrowly defines the role of the player and how he gets things does. Equipment can be changed without limitation when docked, but some equipment requires certain skills.
Randomization, in particular randomizing enemies, their abilities and so on, is a tool that hasn't been used much in MMO's. I think there's a lot of potential to do interesting stuff with it.