You raise some very good points about the difference in terrain between land and sea here. Often at sea there's not much you can do against a large navy given a smaller navy. It often is a brawl to see who got more mele ships. I think that is a dev decision which is baked into civ5.
But I think this is an area where we players can play around the AI instead of hitting it with balance nerfs. The defender can set up citadels near cities to damage ships. Forts and citadels with lands units on top of them tend to draw fire from male ships. I noticed the AI often prioritise clearing units around the city first before going for a siege. So as long as you have units around the cities, that should keep the AI distracted for long enough for your forces to beat them back. Combine this with a road network to cycle your units and your coastal cities should withstand most naval attack.
Yet, even with all that defence, your cities might still get taken by AI. They might get so ahead somehow and have a carpet of ships that your city just don't hold. It is not over yet when your cities get taken. You still got your units around and they're pissed. You don't need to retake the city right away. Let the AI have the cities for a few turns while you take out their navy trying to defend your former city. Your former tiles now serve as healing bulb. You beat back their navy and liberate your city.
Now that's a lot of work, and its hard. But isn't that is why we play? It is challenging and hard but through our wits we overcome it. I don't think the ships need a nerf and I find the current numbers on city RCS to be fair. I believe there are enough things counterplay vs a large navy tactic wise that a balance tweak is not needed.
I do agree with
@Stalker0 that this has to be balanced.
As you have stated, naval battle is basically a look at who has the largest navy as the one with the most ships generally can outlast the enemy through attrition and win that way. That basically means a human player has little to no chance against AI in naval confrontations on maps that requires both an army and navy. We think we can agree on that.
Regarding playing around the AI, we can do so more with land battles than naval battles. Setting up citadels can work but how many citadels do you have available? If you have major land wars, how many can you spare for your coastal cities? If your opponent has numerous Ironclads and it takes them something like 3 to 5 turns to take down a city, do you think that Citadel will do much? Regarding drawing fire, we must remember that naval ranged units have to do something against naval melee units. Therefore, we have to remember that naval ranged units hit very hard and, as the human player, we cannot take such a beating as we cannot replace units as quickly. We can also see that land units can only inflict so much damage, even with focus fire, and maybe sink one ship per turn and that doesn't buy you enough time to save a city. We've seen screenshots by
@Stalker0 and, despite his ranged units, it was a losing battle. Cycling units can only do so much since healing takes time and time isn't something coastal cities have a lot of at the current situation.
Regarding retaking cities, we must remember that some of these cities might be core ones. Losing them means lost infrastructure and being set behind more. Why are we encouraging a playstyle that (a) the AI won't know how to take advantage of and (b) sets you back when you clearly did nothing wrong other than naval units being too strong? Let's not forget about that Citadel which is now aiding your enemy. I'm sure that Citadel is doing wonders for you too if the positioning just happened to make it difficult to reach.
I think people do want challenging matches. However, there's a difference between challenging where you have a number of things you can do to eventually come out ahead (like having sufficient defenses, proper city placements, not falling behind in tech) and dealing with frustrating mechanics that requires some ridiculous response (like losing the city on purpose to whittle down enemy before retaking it, not settling coastal cities). As of this moment, the only real counterplay I read from your post is getting a larger navy than your opponent so you can dominate. Everything else is either less than optimal or just encouraging some really cheesy strategy. I hope I don't come out as harsh but there's no fun to losing cities when you are doing everything right.