1. Navy as a water fighting force isn't useful beyond escorting transports.
2. For the first half of the game there aren't really navies, just ships that can move troops.
3. Yes navies are important on archi maps (which I don't play much) but still only for transporting land troops.
4. By the time you get lethal bombard in the navy (besides dromons, which are very good) you're almost to bombers, which are better in every way. Perhaps the most powerful navy is one of aircraft carriers + escorts, once again in which the non-navy units (bombers) are the main offensive weapon and not the escort.
Final verdict - navies are useful (in getting the REAL military into the battle) but aside from archi maps, not at all essential.
I suspect they'd be better if amphibious assault was easier and more powerful, perhaps some sort of landing craft that allows any unit to go amphibious? By the time you get marines, tanks are better, even if you're transporting them it's run in, drop, run out. But now I suspect I'm just rambling.