Cryptic Studios made clear the basic framework of its vision for Star Trek Online immediately after announcing the game, but the occasional interview or FAQ has revealed greater detail over the past few days. The latest example is a video interview at MMORPG with Cryptic's Jack Emmert, who in the interview reveals specifics about character, race, and starship customization. He also talks about Cryptic's relationship with the previous holders of the Star Trek Online mantle, Perpetual Entertainment.
As far as the customization goes, you'll be able to customize the "skin, eyebrows, antennae, and hair" of your characters and races. At launch, it's likely that all players will be humanoids. Ship geometry, colors, decals, names, and even serial numbers can all be set by players. It sounds like they'll use basic "kits" of tools based on which faction (Federation or Klingon) they choose.
Emmert also says that "war games" within factions would be possible, allowing players to engage in PvP with members of their own factions in a limited way. He doesn't sound at all certain that it will be possible at launch, though.