One thing that was done by Josh on the old UK server some years back was to write an "Official faction payday bot"which would reward official faction players (and the faction itself would get an extra bonus on any bank vessel they had) for activity on each of their ships over the previous month - with players who used fighters getting more per hour than those who flew capital ships (This was done to offset a "lolcaps" style of gameplay that had started to pervade the server back then, with virtually all fights & RP being between cruiser-class vessels and above).
Perhaps something similar could be done for here? Of course, nowadays the faction payouts could likely go onto the faction's main player base if they have one, while the players would still get a cut. There'll have to be a balance done though, high enough to make it worth it for players to login with each of their official faction characters, but not so high that it makes trading characters worthless.