I'd like to see more playable 'canon' species rather than endless customised made up species options. I hear Romulans and Cardassians are in the works (Yay!) but I'd also love some of the following species to be available to play (not as their own faction but as Federation, Dominion or Unaligned/Mercinary species members as appropriate): Ktarian, Breen, Vorta, Farian, Tyran, Miradorn, Tanugan, Coridan, Evora, Yridian, and Grazerite.
Also, though it's understandable for the federation as they have hundreds of member species and obviously Criptic can't make them all available to play, I think aliens should not be an option for the Klingon faction and especially for upcomming factions like the xenephobic Romulans and Cardassians, there ends up being way too many species that never appeared in any Star Trek episode or movie. I also think NPC's should always be species that have appeared in the television series and movies and not random made up ones. The game loses it's Star Trek feel because of it.