I've discussed this before in a different thread, and I like the idea of a flagship battle, but I agree with the above poster who mentioned that 8 crew is probably too much.
But let me repost the idea that I was talking about, because it's very much along the same lines:
"Here's what I would like to see (keep in mind that I'm not taking balancing or ease of implementation into account, just thinking of what would be fun):
3 classes of ships: Frigate, Sky Destroyer, Cloud Cruiser
Frigates: Squid-sized, 3 crew
Sky Destroyers: Pyramidion-size, 4 crew
Cloud Cruisers: Galleon or bigger: 5 crew
Each team would still only get 3 captains, so each team would get one ship from each class (I suppose they could also just get 3 destroyer-class ships, but I'm not sure why they would want to, or how that would be implemented). I think that this could be a really fun way to play GOIO and it would fit the theme of teamwork and role specialization. Each player has a role to play on their ship defined by their class and loadout, and then they work together with their fellow crew to perform their ship's role within the team.
I think that 8-crew ships should be reserved for special boss fights in Adventure mode, but I think that varying crew sizes slightly would be a great way to add replayability to the core game mechanics."
This kind of change can be applied to all game types, but if it were implemented, adding a flagship battle mode would be very simple. Just take the biggest ship on each fleet, and that's the flagship. Or just let each team pick who's going to be the one.