I liked the idea I heard before of indys joining with the Alliance after they get a certain amount of money. The indys shouldn't work together though, cause then they aren't indy
Also, the thing about the Alliance having more ships and being able to put a bounty on people (cost depending on score and what to have attack) is a cool idea. You should just be able to specify a certain amount of net damage (say, 1T) for them to do, pay some amount of money, with more or less cost for higher score. Maybe less cause they can afford to lose it and you aren't doing so much damage, or maybe more cause if they are stronger they'll be harder to hit, and so they'll be worth more. Also, you should be able to pay a certain amount to have them go after the player's ship. That'd be a cool idea. The Alliance should get its strength from Indy planets that join it after they get to a certain strength. That way, the Alliance won't be all powerful, but will grow as the players grow, because as the players grow so do the planets that go indy on 'em.