Well, 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):
Muse upgrades their servers so that 24-player matches become the standard.
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.
That actually sounds really good! Keep going with the ideas! I'd like to see something like that too.
I see one problem on first place though: For the big and the small ships you need an experienced crew if you think of it like Squid and Galleon. The Pyramidion is an easy ship, so everybody can fly as well as be gunner and engineer on that one, but a Squid and a Galleon... I don't quite think you'd get the teams filled. There'd probably be many games with the Destroyer ships filled but empty small and big ships. Furthermore, if for example I wanna play with some friends but we both like to fly Squids...well, it'd either not be allowed to do so or make balance too difficult to calculate.
Since I don't think that the bosses in the Adventure mode will be playable by humans, I really would like to see them in skirmish at least, so we can use them (or at least one).
Going into the balance issues (and yes, I know you just wanted to present your idea,
which is really good!, but just showing every side of the possibility Im gonna write that down too), I don't think that 3 people on a Squid are enough to keep it alive - 5 people on a Galleon though makes it almost invincible as the ships stand now. Only making 1 big and 1 small ship available for every team destroys some different tactis though, and making them available in any mass is...well, just as we do now but with different crews (see above).
I'm not even gonna start with implementation.