And remember, EoN is not an AoS game. It's an RTT with very extreme RTS hybridization. The RPG elements are extremely dulled down to keep the RTS feel. There are no creeps here and for the most part, little NPC involvement at all. Employing the use of "lane styles" would be foolish here.
Also, in terms of player enjoyment, you won't want to force many players to do something they don't want. Many here are fine without a Navy to use, and having maps where the Navy is included along side the land battle would force players to HAVE to use the navy to get an advantage for their team. By keeping the Navy confrontations separate, you keep the combat pure to those who WOULD enjoy it; making it more fair to the player. This would mean that there maybe far fewer Navy players, yes, but the battles would be far more pure and fair and would display equal results in terms of capturing territory.
The idea is to give player's the "option", but not force them into that choice.