If there were Dev resources, I'd campaign for an ELO-style hidden ranking system for Battlestations that assigns each character a 'rank' that is based on a variety of factors related to their performance in PvP. Then attempt match-making by distributing people across the teams evenly based on their rankings. Rankings change over time of course, depending on how that character performs, and the idea would be that a twinked character would be put in a team opposed to another twinked character. Pre-made groups would automatically be given the highest ranking and therefore be put against the best of the non-premade characters. Could even attempt to balance professions somewhat, such as profs with healing being distributed evenly. I've seen that system work reasonably well elsewhere.
Sadly that would also require 1) enough people that would want to participate and 2) having the 3 teams be completely faction-independent. To solve 1) needs major kick up the backside in terms of incentives, though I'd hope that having a match-making system in and of itself would help to encourage people too. Bit circular there. To solve 2) that ought to hopefully be an easy code flag. It won't be popular with everyone of course, especially people who want to keep an RP head on. But for the sake of balance and matches actually running, it's a necessity. (RPers can imagine it's just a training sim )