Here's how I'd do it: (assuming an Xwing style engine with 16-64 players)
I'd have a zone where anything goes PVP.
I'd have a zone where it is team play(even teams)
I'd have a place called "Invasion" team combat. You start in neutral space territory. Then survivors advance to a place where they fight among a capital ship firing back. Then if you win this, you fight against a space station. Basically the match is even. Then the match is in favor of the losers. Then the match is really in favor of the losers.
You can even go further than "Invasion" by allowing multiple teams on multiple fronts to fight, and depending on their results, the galactic map changes. Take a clue from Global Agenda, but design and execute a bunch better.
The biggest problem with RPG+Action is that eventually everyone has maxxed out gear, and it still has to remain fun. If you design with this in mind, you can make a game that will last long enough to suck in the next generation of gamers. I've been waiting since the Red Baron days to have some sort of Flight Combat simulation that was MMO. So far no one has delivered.
PS: I'm a professional video game developer and designer.
Just thought of something to add on: You could even have a hybrid space shooter and land based mission like Invasion. Say you do space combat, then you need to capture information from inside the space station. You'd even have land based PVP too