I understand it would be really really hard to do it but adding subs would add a whole new dimension to the game. add depth charges to the ships in the fleets and pt boats; heck what about a gv that could lauch DCs into the water defending a port too?) Maybe some more AI convoys to hunt with subs. And even player resupply convoys of transports with some armament; players could always team up with escorts for added safety. maybe another launchable craft (like PT boats) but bigger and costing a few perks)+resupply transports could rearm/repair subs just like an m3 can resupply/repair friendly GVs
If you'v ever heard of the older mmo 'Iron Wolves' (you could use subs, transports, destroyers, cruisers, and some other stuff I think); that was a great game for its time and like I said would add a whole new element and even attract more players to AH.
Heck even add a new class of perks : it could be fighters / bombers / ground / & ships (not sure what rescue choppers would fall under)
(could make perks earned on fleet ships and PTs go to the ship category as well as points from subs and transports)
Could even add depth charges as aircraft ordinance in buffs and certain fighters (salvo | delay | fuse/depth)
And DC launcher player positions on fleet ships