The Star Trek Online official site has been doing a great job laying out how the gameplay will differ from other MMOs. For instance, their recent updates explain how ships will work.

Ships in Star Trek Online are as much a part of your avatar as your captain or Bridge Officers. They're highly customizable, both cosmetically and functionally. Visiting a ship "tailor" will allow you to change the color of your ship, the nacelles, the neck and/or nacelle pylons, its saucer, its name, its registry number and so on. And since ships have paperdolls and Bridge Officer stations, the decisions you make in how you outfit the ship's weaponry, impulse engines, shields, deflector dish and mods guarantee your gameplay experience will be unique to other players, but at the same time still feel like Star Trek.

A cynical MMO player might see parallels to things in other games. For instance, he might think of crew as a counterpart to stamina or mana. He might think of bridge officers as a counterpart to gear or equipment. But even then, a cynical MMO player has to admit that not even Eve Online takes this sort of approach to commanding a starship. And if there's one thing a cynical MMO player would be interested in, it's seeing a game try something different. I'll bet dollars to donuts a cynical MMO player will be waiting in the login queue to see how this turns out when it's released early next year.