Okay, so I went through a few games trying to see if this problem was fixed as you seem to claim, but its not. Yes, there is a 'Flagship' in the game. When i read my post now, I guess I didnt state the real problem clearly. My suggestion was a way to fix what I see as a problem, but also took the opportunity to add game mechanics. I direct your attention to this thread: https://forums.sinsofasolarempire.com/343452. Top half. thread kinda got hijacked the other half.
If you still dont understand, do this quick test: build 2 capitals. put them in a fleet together. try to assign it to a number in such a way that the second capital constructed is the default ship selected when you select the fleet. You cant do it. Heck, if you push the fleet icon, it doesnt work. The game prioritizes based off when the capital ships were built. It doesnt matter if you disband and reform the fleet, the only thing that can fix it is to get that first capital ship destroyed.
I understand that it seems pretty simple to tab through till you get what you want, and I do tab through. I'm just saying it'd be nice to set what comes up by default so I might not have to. I know I could assign each capital its own number, thus giving me the ship I want. I sometimes do this, but I like to play big games and have too many fleets going around to do that correctly. Besides, it currently doesnt make sense. When you select a fleet, the flagship should be at the top of the stack (or default ship).