Star Trek Online is adding a new system to improve matchmaking for PvP. The new system, known as the Player Potential System, calculates the potential of a player by taking their equipment and specializations, and combining that with a special modifier that is generated when they play competitive Ground or Space matches. The more matches they play, the more data there will be for the system to work with. This means that as players compete in more matches, the matchmaking system will improve.
The developer post on this system does note that players will experience a lot of variability in their matches, at first, as the system works to get a bead on their abilities. As they play more matches, the system will tweak the calculations as a player competes in PvP to assure more balanced matches as time goes on.
They also add that the system is smart enough to pick up on if a player is winning or losing too often. If this happens, then it will drastically change their Player Potential.
More details on the this new system are available on the Star Trek Online blog.