Tactical, Engineering and Science; the three main career options when starting with your new character. I'm aware this is likely to end up as a potential long-term agenda, but I'm thinking these options could be expanded upon.
In my opinion the Federation should be Engineering focused, the Klingons would obviously be Tactical focused and a third faction (hint Romulans) should be Science based. We'd still have all three options for each faction, though a Klingon player who has chosen a Tactical Career would maybe get a little bit of a bonus in some way?
If not that, then I think it would be worth looking at how different factions play. At the moment, the one and a half factions that we've got all play the same. Shouldn't Klingons feel more warrior-like? Klingons should be more warrior-focused with their own unique captain abilities (rather than a general set). Same would apply to eventual Romulans; base their captain abilities around stealth maybe? Just something to differentiate between different factions, thus if someone owns different toons for the different factions, they'd have some variety other than appearance and social maps; gameplay should feel different too.
I'm aware this probably wont be no easy job, but I think in the long run it would make the game community a happier one. I know I'd feel better having different play styles.