The major problem about naval forces is that they form a parallel layer to ground forces. Naval and Ground forces, being restricted to different movement surfaces, can interact only superficially. Basically, you have two games held together by the shore line. Contrast this to air forces which, while having different movement rules, act on the same layer as ground forces.
If you look at the design of RA3, amphibious units are a major key in its gameplay. This serves to lessen The Divide between ground and naval forces and allows for fluid combat. A realistic scenario such as Gen2 doesn't allow much leeway here though, you could have some small hovercrafts and amphibious vehicles such as APCs, but actual Navy could not be consistently integrated into the existing gameplay.
Really, I think the way it was done in the Gen/ZH campaign is best. SP allows Navy to actually work at its full potential without upsetting balance, but even then the fun part is ground combat.
Could have them as sort of a capturable "building" in the water that confers some bonus, bombardment, extra vehicles maybe? But then to make it balanced the GLA would have to have some good way of getting out there.
I think it would be concievable for the GLA to have naval tech on the same level as the other factions, or at least as far as hovercrafts or whatnot go.
Not sure how one can rationalize ships just waiting to be occupied though. Still, come to think of it, small scale aquatic transport could work in the game IMO.
By the looks of things, Generals 2 probably happen on 90% dry land.
If we prove that we actually want naval gameplay in the game then what could we do to get the developers attention, start a petition, or spam their inbox's.
But if they don't implement it then we may not see it until Red Alert 4 comes out.
Personally I feel that adding Naval units would be a big blow to the balancing of the game. And many have stated above, it does house a lot of problems, and for Bioware to deal with them I suspect G2 might just take as long as Starcraft 2.
I feel that if the addition of Naval units is a must, then let it be only for utility uses. Eg. Transportation, Aerial defences, General powers etc. Let me justify my point: If the naval units are made solely for utility uses, the game would not be too unbalanced in a sense that everyone just spams Naval to counter ground/air units. Not only that, it brings about a new way to disrupt the enemy/giving you a slight advantage such as surprise attacks by sea, or perhaps block off a sea route with aerial defences to make sure those pesky aircraft do not sneak behind your front line defences and drop some aurora bombs in there.
Just my suggestion, though.