I personally enjoy [member="Cradossk"]'s suggestion, as well as [member="Siobhan Kerrigan"]'s, though she brings up an even hairy point up:
Has staff actually engaged with the Flashpoint idea? I mean, I am aware that we'd only get a single flashpoint for every ten invasions/rebellions statistically, but it has been a long time since I've seen anything different imposed by staff on either an invasion or a rebellion. Has there been a Flashpoint yet? I haven't been aware of one happening, so if it happened it must not've been super well received. I also disagree with the idea that a rebellion could be instantly crushed, that seems more gamey than is necessary for an RP board.
Regardless of that, I think it is better to impose incentives on things, as opposed to creating rules of limitation. As rebellions currently stand, they are rather bland. Sure, if a rebellion wins they could ascend to major and gain a hex, or keep the hex neutral, but for a Major faction it was just a lot of headache to gather the equivalent of an ordinary dominion, and more than likely if they were going for a Flagship, it will be so delayed they will be denied it entirely just by the rebellion existing.
Siobhan's suggestion fixes much of this, by making an incentive for both sides to give their all and win. The rebellion should be motivated because if they win, not only do they get to decide what happens with the hex (and potentially gain an SSD right away if becoming major), they have also prevented the Major from getting additional hexes if the Rebelling faction had lost. For the major, it is patently obvious how it would benefit them greatly to be victorious, as not only do they get extra expansion to make up for potentially lost Dominions focusing on a Rebellion, but also acquire an SSD at the conclusion of the Rebellion, something they were potentially seeking prior to the Rebellion's intent being initiated.
I believe this would be a better solution that could make people more interested in a rebellion, as opposed to limiting how many can occur for minor factions, which are rarely active enough for more than one anyway, and gives them a potential thing to "lose" by failing to be victorious: their IC enemy grows stronger because of them.