Apart from stopping reinforcements? You say that as if that's minor. The invader stack can be countered and defeated usually. It's the reinforcements that drive the nails into your coffin. Destroying the enemy's navy keeps them from reinforcing their front against you. Pump out naval vessels and use the Nationhood civic to draft desparately needed reinforcements, and you'll counter the invasion stack. Keeping reinforcements from making it across, preferably taking the ships out with their armies on board, will make their military more stagnate while you build the counter attack. I played a game once, where I had the only oil on land, and my destroyers kept the sea clear of enemy improvements. Overseas enemies with armies large enough to stomp me, had no way of getting them to me. The powerful navy is not the one with more ships, but the one that makes the enemy suffer more. Keeping their bellies fishless inflicted more damage on them than the sinking of their navies did. A powerful navy is one that makes your nation the only one in the world that knows the taste of fish. Invasion fleets are overratted, and underpowered as it is. I stopped using navies offensively, ever since they made ships unable to attack units on the shore. In Civ III the formula for overrunning a civ, becomes, build X units per city, then invade, and the formula for invading overseas, is Build X units per city, then put them on boats, and send them with a few destroyers to keep the transport stack from getting sunk by the other civ's ships. Suddenly naval warfare felts so undertoned. What I found amusing in Civ III was when a larger civ would declare war on me, then send a bunch of warships into my seas, and just sit there, not doing crap except blocking out a coast square or two, not able to do crap to my port cities' defenders but take a hit point off ever two turns, just to watch it go back up. I was just on the floor laughing... In Civ II those same units would have whacked my sorry ass out of the ports, and ships with units to take the cities would have arrived within a few turns. Instead, 15 turns later, my units are upgraded, to the next tech level, my destroyers clear their ships out, and their massive stack of Cavalry and Knights just does't stack up to cities defended by Infantry.
Civ IV is better about the "One Infantry kills the Cavalry Stack" canundrum, and has an improved version of both sea economy and naval intradiction. In Civ III and ealier games, naval units stopped trade on the square they inhabited, but in Civ IV Naval units stop trade on the squares they inhabit, and the adjacend sea squares, so Civ IV has a sort of "Zone of Control" for naval units, but it is in the department of trade intradiction rather than stopping units. If you put a ship in every third square, with one free square between each ship and the coast, all along the coastline of an enemy nation, then that nation has no sea trade whatsoever. The way the oceans are handled is not underpowered or overpowerd, it's just balanced in a matter that works differently than the sensibilities of land army tactics. The idea is that land combat, and sea combat are inherintly different, and the very objective of sea combat is different. I don't usually build my strategy around having a powerful navy, but I do like to enjoy the benefits. And I rather like being able to drop big stacks of units on my enemy's shore, on the first turn... and if I have a crapload of marines to fight with the first turn, even better. It's not like the game doesn't already have enough handicaps and defense strategies that put the odds inherently in favor of the defender. Ever heard the saying that, "Invasions are not stopped by great pitfalls, but by friction." Every slight delay, and setback, creates just one more bit of friction. This is good for giving defenders the ability to keep themselves from being totally wipped out. But putting too much "extra fricton" will sipmly make offensive warfare more tedious, and it will ultimately do the same for defensive warfare. Giving the defender the chance to prepare his counterassault on the first turn to weaken the offenders, will only result in the offender anticipating that it will take more ships(which means more troops) to get beach head, which ultimately means the AI, which is both repetative in its behavior and has no sense of the tedium, will simply build larger navies, holding larger armies, with which to smoke your ass.
Which brings me to my point. Making ships unable to land units the same turn they move, will simply add yet another point of friction to the warfare process, which will simply make wars more tedious and drag them on for longer, without actually adding anything, but a potential point of convenience for the prepared defender. If you have enough ships to take out the invasion fleet, then don't bother being the passive defender, take their ships out first, even if it means declaring war... and if you don't have enough ships to do that, then a "one-turn delay" won't help you one bit anyway.
Naval Transports (Galley, Galleon and Transport) can just wait at your bolder then declare war, move to the coast and drop all units on your land in just one turn - before your naval force can move a bit. Right, you can declare way on him when you see enemy naval transports are gethering near your bolder, but that way, it's you that are responsible for the war. That means you can't stop enemy first landing even if you have a overwhelming naval force. 
Naval warships are useless enough, I think - they can't do anything with enemy landing neither.
To make the warships could stop the transorts, I think, is to stop transports drop troops at the first turn in a war.
