Well, I'm thinking, for like co-op, that a mastery system in League of Legends or perk system in Sanctum 2 would be pretty nice.
I mean, when you are facing humongous boss ships with your tiny squid, you're going to want some passive buffs that makes you heroic.
But that aside, one of my ship design pet peeves is how things are "out-of-the-plain-sight" on a Galleon.
I can't count the number of times when I had to show a new player where the bottom deck stairs, bottom deck ladder, main engine, and the aft guns were. When you've flown on it once or twice, its fine, but every steam sale... It's just my pet peeve.