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.