I suggest these things:

1)  give apa some sort of experience for the damage they do to the islands/hq.  (if we don't capture hq, apa gets nil for xp and really the apa's focus is on capturing not damaging other ships)  the other ships get xp even if we lose because the do damage to ships.

2) put a 2:00 timer on after the last kill (like gb2) to allow the opposing team to capture the enemy base (or go as far as possible)

3) (somebody else's suggestion:) if you shell the enemy hq it becomes neutral and needs airlift or landing force to capture

4) (maybe not so serious) give negative xp to the ship that sinks the last enemy ship on the map. (so they see -5000 xp at the battle summary and their sailors go backward.)