IPOD connectivity on captains chair, pedistal to the left of captains chair with orion slave girl, mini skirts to be COMPULSORY for all female crew members, ready room, quarters, housing at earth or any other federation planet, Risa would be nice.
More ships but no less customization, and the option to choose from 3 colours for all phasers on FED ships, 3 colours should be the traditional orange the classic aqua blue and the Vulcan green, pink is totally a NO NO.
The Klingon Tribble Predator (Filmation Animated Series: More Tribbles, More Troubles)
A neck/mouth attachment for Androids from the Planet Mudd with a number you can enter in to show up on the front. With a keyable emote that makes it flash, as though your character is in thought. Or maybe just Mudd Androids as a playable race.
I'd like 'The Game' back as an eye attachment.
Cybereye implants like Geordi LaForge had in First Contact as something you can choose for an eye option.
Catians. With the tails and everything. I'm not a furry, but I liked me some Lt. M'Ress from the animated series and the DC Comics.
Classic Uniform Variants. Like the William Ware Theiss uniform from the classic series. The Star Trek: The Motion Picture uniforms. The Red & Black uniforms from Star Trek 2 - 6, with the cool as hell expedition coats.
Classic Weapon Variants, from the old Wa-Chang pistols to the newer 'baretta' style pistols from ST6.
Many Many more hair options. Including 1960's-Tastic Updos and the Janice Rand Beehive
As far as carriers go, they were established in a Playstation fighter sim game, "Star Trek: Invasion" where you were flying in squads of fed fightercraft from theater to theater. One would think that since the game fell under the aegis of Star Trek related materials, that Atari would be able to get permission directly from Paramount to use them in this game.