Having just watched some of the PAX videos, I'm getting pretty excited about this game. I do, however, have a few issues with the seeming ineffectiveness of evasive maneuvers (does every single shot have to hit home? This is a big annoyance of mine in EVE as well.) and, as other people do, with the partial 3-D space which doesn't allow rolling or AFAIK vertical maneuvering like in Star Trek II or the Homeworld games. Still, it looks great and I'm very much looking forward to getting to be a participant in this form of the Trek universe.
It depends on the size of the target, they've said that both phasers and torpedoes can miss smaller ships. Officers can also obtain skills such as sensor jamming, if used against your vessel for example, it would stop you from automatically targeting an incoming ship, so you'll have to manually target enemy ships instead; this is quite a powerful tool for smaller ships.
Then you have certain ships like BoP's, who will work together as a group and focus on one shield, all the while cloaking and de-cloaking. Once they have a shield facing down, they will start hammering the open spot.
The whole area of space you fight in is also fully 3-D, a ship at the very top of the combat area would not even be able to pick up an enemy target at the bottom of it on their sensors. When ships engage in combat they try to remain roughly on the same plane (like in most of the TV series) but you are fully free to go where ever you want, if you feel like it.