I added a couple of Onslaughts to my roster (and maxed out the battle size slider), since the top-end bounties and such now feature titanic ultra-fleets, and soon enough ran into exactly the issue I knew I'd run into: fuel. Its specter has been lurking around for this entire campaign, haunting me, whispering that when it came time to field multiple capitals, this playthrough would pretty much be over.
I haven't run out of fuel yet, but the huge stockpile I'd saved up in anticipation of this is now gone, and it's pretty much inevitable the next time I have to go anywhere. Hegemony space has too little fuel production to support a large fleet, unless perhaps you park almost your entire fleet and run around with tankers from one system to the next grabbing whatever you can get (and hoping you don't run into pirates), but that's an annoying waste of time. Loot and salvage fuel, even in systems stuffed full of automated encounters and such, only helps to put corks in a few of the holes in your tank.
If you're enemies with them, Sindria isn't an option, period. You can't get tankers in there if you're enemies with them, because tankers are slow and huge, and you WILL be caught by patrols. You can't sneak in, because a sneaky small fleet has zip fuel capacity. You can't even fight your way in—I tried, but of course there's a "You've created a disturbance! That's a one-month docking cooldown!" developer hand-slap in place for that.
I guess if I'd known the game mechanics better earlier on, I'd have sneaked lots of AI cores into Sindria to try to get on their good side. I just don't understand why you aren't allowed to have enough fuel to play the endgame unless you're friends with Sindria. It just doesn't make any sense. This is with Navigation 3, mind you.
Maybe I've missed some other way apart from tootling back and forth with tankers slowly sipping up whatever's in each Hegemony star system? If not, I think I may declare this first playthrough finished and try out Nexerelin, DynaSector and some faction mods.