A lot of good ideas here. While I agree that it's desirable to create mechanics that make faction-war servers run well, I would like this to be a game-mode choice for each server not straight up vanilla. My only real concern is that all vanilla game-mechanics allow for all styles of play.
Just a reminder: there are a thousand ways to play a sandbox game like this. I hear a lot debate that seems to assume that faction-wars are the only,best or most important game-modes that people use.
Again I support this concept, so long it works for build-servers, straight RP, single-player, event-servers etc as well as the RTS/faction-war/Epic space-opera.
Of course, the amount of FP drained by this would be configurable, leaving the option to set it to 0 and disable the feature completely.
However, as I see it, the system should probably be enabled in vanilla... In the current state of vanilla, you can somehow "own" a system sustainably despite pirates (or even enemy players) maintaining a far larger presence in the system than yourself. Having to destroy enemy bases to claim a system would, in my opinion, be a really neat part of establishing your faction and place among the stars, and would make the deed far more rewarding and meaningful in the end.
...Also, the mining bonus mechanics need to be looked at, I think, but in the meantime players can just activate their system claim, mine, return to base, and deactivate the claim before significant amounts of FP are lost to enemy presence.