A couple key gameplay changes for discussion:
1. Each ship has one designated target on the opposite side. That target can still bombard any ship on the same side.
2. Ship cells can only assault their designated target. They cannot assault adjacent ship cells.
#1 does to things - it makes it more difficult to gang up troops on first turn and take an opponent's ship (which would be unlikely, but not impossible). Second, it adds some intricacy to the assault strategies and a reason to have more than just one or two targets on each side.
#2 makes the impact of a "Hit" more like the game. That cell is out of play once its hit. If ship cells can assault adjacent cells it will drag games on when you can just take back the neutral 1 each time. It really isn't needed, since the bonus only requires one cell of the ship. This makes it more realistic without really changing strategy.