I think customization of a character in an MMO is possibly one of _the_ most important elements. Especially once a large chunk of the population has reached 'end-game' levels. Players want a feeling of personal ownership in these virtual worlds. A sense of uniqueness. In a sea of pixels, people like to stand out and be noticed and noticeable.
Everyone can have a blond, female Betazoid... with mysterious Green eyes!! ... woOOo... but, not everyone would think to make a blond, female Betazoid with mysterious Green eyes, who is sans an arm after a recent encounter with the Borg. So far, STO has had a decent array of skins and costumes, body shapes and sizes, but I think expanding these individual options would really give the game a boost. AND!, give a lot of the end-gamers something to do.
The same can be said for the customization of ships.
It seems like the infrastructure is already in place, and maybe it would be as simple as 'unlocking' more options within the customization windows. To some extent, the character modification screens are akin to some recognizable consumer-level 3D modeling programs. (think Poser Lite). Why not take the next step and make each character completely unique and crafted almost from the ground up by the players? Why not allow players to scale and position, color and shape some add-on ship elements?
You guys are on the right track with the Borg ship modifications coming out soon (kudos to being able to toggle them off or on, too!), but, pretty soon, everyone will have those same mods, and seeing that cool looking 'Borgified Sovereign' will become an everyday occurrence. If you expand upon this modification concept a little further, by, say, allowing the player to shape, scale, and position these Borg tech parts on their own, you would really push the individualization and feeling of personal character ownership to a whole new level.