One of the striking things about FTL is the capital ships you see in the main menu, in the background when the rebel fleet has caught you, and during the final battle. In those systems where you've been caught by the rebels, you get attacked by one of their vanguard fighters and have to retreat away before their cruisers get into range.
This strongly suggests a fundamental difference in size and power between your ship and the cruisers. They're much MUCH bigger and more numerous to the point where you can't hope to fight them. I liked this a lot - it's very critical to the game's theme of 'run away and try to survive' that you actually are pursued by a real danger, and that no matter how powerful you are there's much bigger fish out there.
I told you that so I could tell you this - SPOILERS BELOW:
Anyway so during the final battle you see the lynchpin to the Rebel success - and it's not that much bigger than you. Instead of a cruiser with a crew of hundreds, or thousands - it's a superheavy fighter. While this is so totally a nitpick, I think it's kind of silly. How many stock Kestrels would you need to take it out? It certainly doesn't feel like the sort of overwhelming force that could bring the Federation to its knees. Moreover, it makes me think that if this is the ultimate weapon in the Rebel's war chest, I shouldn't really have been fearing their pursuit. I could probably have taken out those cruisers that the game tells me I have to run away from.
My suggestion, then, is this: I recommend a few minor text/story tweaks. There's no reason or need to change anything about the scenario itself. Instead, say that the Rebels have been able to annihilate key Federation fleets and planets in seemingly single strokes. That secret is that they have a very powerful, advanced, stealth ship with weapons of mass destruction. When talking about this with my friends, I considered antimatter bombs. With this stealth ship, the leaders of the rebellion could sneak into Federation fleets or up to Federation strongholds and vaporize them instantaneously. This is why no amount of capital ships will be able to stop this ship, either, because it's got a supply of devices that are great at destroying large slow targets like planets and battleships. The player is still important - the enemy ship is a small fast ship among many in the Rebel fleet, and the Federation heavy ships have no chance to catch it, especially if they're busy with the Rebel cruisers.
So nothing changes about how the game plays. The rebel super-bombs explain why the repair bases fall; it's not because this mothership has that much raw power, but because it literally has a bomb that can destroy anything. They also don't want to waste it on one relatively inconsequential fighter (your ship) because they're hoping to take out the final Federation base. I might even suggest that the special data the player ship has is the transponder codes of this ship and thus can track it. Perhaps the rebels won't hit you with their super-bombs because they're running low - this final battle is just as desperate for them as it is for you, because they only have enough left to destroy the remaining Federation bases and fleets.
There's a number of other possible variations- in the end, what I really recommend is coming up with any scenario that still makes sense, but doesn't make the player think that the most powerful ship in the Rebel fleet has less than a dozen crew. I'd like to imagine those big ships out there are giant space battleships, not the same sort of Space Winnebago that the Kestrel is
So maybe it's just that this ship is a prototype super-fighter that houses their leadership, and taking that out is enough of a morale hit to give the Federation a chance. Again - this is a REALLY minor nitpick, but it's something that I thought I'd mention. I can't think of a single bit of gameplay this would change, only story in the final battle. Plus I think I like the mental image of two small ships hunting each other amidst huge fleets of capital ships fighting in the background better
Thanks for reading!
There's definately going to be a compelling reason why you're the only ship that can save the day. We're exploring some options at the moment - watch this space!