Of all the RPG's out there, the current "rules lite" system with the most active support and grates flexibility looks like Savage Worlds
. (Disclaimer: Myself I prefer Hero and can't stand the "not quite finished unless you buy yet another book" GURPs
) That all said, I do really think adopting something similar to SW would suit most mini gamers best, I was able to GM a full session within a day of picking up the rulebook and it flows well and things can easily be altered on the fly.
SW is at its core a genre-less system easily adaptable to many settings, with a very large range of different setting already available from Weird WW3 to Pulp Space to Cthulhu Horror. They are close to re-releasing a Savaged edition of Space 1889 as we speak.
For MJ12 I would recommend a Savaged source-book for its world/settings. Many source-books/settings add unique rules/options as well. The basic rules are short and cheap, the PDF is only $9.99.
I would like to see MJ12 bring something to the gaming world that I have not see successfully done before. A way to merge the Role-playing with controlling ships on the gameboard in a SIMPLE manner without tons of rules. I am primarily an RPG gamers that had almost given up on mini's because most rule systems were so complicated they just sucked the fun right out of the game. I still read and loved my history books and scifi stories, but it came to mini gaming the drudgery of assembling and painting ships/armies just wasn't worth the effort because of the overly complicated completely un-fun rules out there. Then, I discovered MJ12. Starmada, Grand Fleets II and so on. The rules are crunchy without sucking the fun out of things. Simple yet detailed. Or in other words FUN to play.
I for one would love to see a plot point campaign for Iron Stars or Starmada. Especially if it contained rules for integrating role-playing directly with ship combat and maneuver.