You know what was cool about the mirror universe? Evil twins!
Whether it is evil Spock, evil Kira, or evil Archer, evil twins are what made the mirror universe really cool.
So what about YOUR evil mirror twin? That's right, YOUR twin from the mirror universe! Why not have a mission where you go to the mirror universe, and you have to go up against your mirror twin.
I imagine the game could easily copy your character design and stick a goatee on it...or, if you already have a goatee, remove it.
It would be neat to see dialog screens with your own face on it, taunting you and committing terrible acts. Your evil twin could also have evil versions of your bridge officers! How fun would that be?
Your evil opposite could also be a recurring villian:
Episode one (as a lieutenant): You and your away team beam down to a planet on a routine mission. An ION STORM forms, and when you beam back to your ship, it is actually the evil mirror universe! You have to fight your way back to the transporter room aboard your own ship, finally squaring off against your evil twin.
Episode two (as a commander): Starfleet has been sent to arrest you! What?? It seems you've been accused of many crimes lately! You are now on the run from Starfleet (who you refuse to engage in battle) and must investigate who has framed you. Finally, you discover that your evil counterpart has beamed over here from the mirror universe, and that framing you is just phase 1 in his sinister plan!
Episode three, four, so forth and so on. You keep having to face off against yourself. I think it would be a fun idea.
I remember a game i used to play title escapes me right now, but the twin matched you move for move you attack; he attack, you heal; he'd heal but it was one of my favorite battles of the game. now im going to have to go try and fig out what game and play it again