I've been playing this mod relentlessly since I discovered it less than a month ago, it's awfully good and so well thought through for every faction, and with exquisite detail in the new designs. It feels simultaneously faithful to Tolkien and to Peter Jackson.
This suggestion, if worthwhile, is very much low-priority because it is a topic that isn't relevant for most maps. I've always felt that the ships don't quite work for all of the factions. Could certain factions have different skins?
The existing Corsair ships work for Mordor and Haradwaith, and the Elven ships obviously for the three Elven factions.
Gondor: has a rich naval history to draw from, whether Numenorian or more recent.
Rohan: perhaps some sort of anglo saxon or Viking inspiration? Or else the same naval units as Gondor?
Dwarves: Perhaps something Dale-oriented?
Isengard: Purely speculative, but if Saruman had ever have the chance I'm sure he would have gone for ironclads, and of course something explosive, though the existing exploding ship already in BFME2 looks more like a Misty Mountains type vessel.
Misty Mountains: The hardest to figure out, though there is the potential to be off the wall and wacky. The exploding ship looks like a Misty Mountains unit as mentioned above.
As mentioned, this is very low-priority, as in almost all maps naval units are not needed or used - not something to look at until very late, if at all.
Only other thing I can think of is that the Balrog is a final tier power for both Misty Mountains and Mordor, when all other factions have exclusive final-tier powers. But I can't think of anything better to replace it in Mordor's spellbook!