Okay, I know nothing about this project other than what I've read in this thread, but if something like this hasn't been already done:
Would it hurt to give us access to Best Ship (i.e. the Pegasus) in more than one mission? Like, for example, in the last arc, when you're supposed to be this big fancy squadron leader who has his pick of craft? Never understood why they did that. And if you're only going to pick one mission, why "Endgame"? It's not like that's a particularly stealth-oriented operation.