Although I'm not much of a sea person (where's Gunboat? unless...) when it comes to Advance Wars series, I prefer Cruisers as my favorite. They are probably the most dangerous unit when it comes to sea/surface to air combat. They can easily wipe out any kind of air unit (including seaplanes) in one or two attacks. They can attack Battleships and Carriers (not damaging, but at least something than nothing).
And they can really get rid of those Submarines. Annoying little buggers, they make quick work of any other sea unit, but they can be easily pwned when Cruisers are around. The weakest advantage point on them is that they don't work well with countering attacks, even strong air units might have a shot at them. Either way, I still like them as the best sea unit in the game.
However, the Battleship is probably problematic in this game as well since they can counter the Cruiser with the move and shoot movement, which made them a whole lot dangerous than the previous ones. Nintendo sure know how to even the odds.
i like massing like 4 or 5 battleships with 2 carriers and some cruisers to keep those pesky bombers away from em the only time i use gunboats
are when the enemy has a bunch of cruisers lol swarming the cruisers with a bunch of gunboats.