I think the example Dez laid out above would be a really sought after feature for my preferred style of game play, it really is extremely more complex and a whole other feature and major addition t the game.
I'm thinking much more simple terms right now to give a Flagship to the player base while short circuiting many of the downfalls that has been brought up.
Make it easy... allocate X crewmen the EXP points and qualities that would be bestowed on the ship of choice. I thought perhaps around 200 crew which is around the crew size of a Lrg Frig. These are the little things that can be sorted out. It could be even more interesting if those 200 crewmen were to be split up into 3 Sow's or keep together for 1 good Lge Frig.
I'm not trying to stray too far from the basic premise of a Flag Ship but rather, consider idea's that could bring it to fruition and keep all that sail a ship benefit.
Edit- As i ponder the idea I just posted, I cannot stop myself from expansion thoughts regarding the idea of having a Pirate fleet of Brigs that could take on a medium guarded trade fleet and win.