I agree that this sounds likely. Here's a refined version of the idea I've had in my head for the last couple weeks:
The ship allows you to sail to a Clan Base. This base can be modified and upgraded by anyone in the clan.
On defense, this is the base that you and one other clan member will use to defend against another clan in multiplayer battle.
On offense, you and a clanmate will attack another clan's Clan Base. You search for a match the same way you do in single player matchmaking. But this time you will only by matched with larger Clan Bases that you can attack simultaneously with your partner.
The clanmates on defense get to watch you guys try to dismantle your Clan Base. After this you get to attack and they can watch. The winner is the clan that has more stars. If stars are even it goes to % damage. If that's even its a draw.
Rewards for clan battles is anyone's guess, but may be gems, loot, xp, or things that are specific to the Clan Base. Maybe the loot you earn via these co-op challenges can only be used to upgrade your Clan Base.
Anyway, just a thought.
