It maybe easier but I feel it also greatly reduces some of the strategy in a game. If you can simply cross any size body of water at any point, with little more than the cost of some extra movement and temporarily weakened them, it makes it practically meaningless as blocking terrain. If you can make boats out of thin air then why can't we cross mountains? Armies have done it in the past to surprise the enemy so it's more reasonable than fashioning boats out of thin air to cross an ocean. Armies have built make shift rafts to cross large rivers before so that is understandable, but boat to cross whole oceans and practically instantly.metamorphing into boats is better than having to be loaded - from both the human micromanagement dept and from the AI cant do it effectively perspective.
I can understand wanting to reduce the hassle of building transport ships, moving them into position, load troops, sailing across the ocean, then unloading troops. But if we are going to do away with building and managing transport ships I think a better solution is having it so troops can only enter onto water as transport when they are in a city with a dock. This way those cities act as important bottle necks and have greater importance to the overall strategy.
In the old Civ days with transports the water acted as a much better barrier. Now it's only a minor inconvenience. The effort of moving a massive army across the sea should in fact be massive. All you need to do now though is make sure the area is clear, which it often is, then quickly sail across. If the area is not clear then use your navy to simply sink the few ships in the area and begin the crossing. The only time it's really a problem is against a good player who has parked a large force right along the coast. In which case you just find another coast to land on.
The more I think about it the more I think a compromise might be in order, simply having both. The make shift boats that can be launched anywhere are weak and vulnerable, they also only last for a limited number of turns so that when time runs out the units switch to drowning. This way the make shift boats can only cross small bodies of water. Where as the fully built dedicated transport ships were more heavily armored to carry troops and have so such life span restriction. I think the problem comes from wanting to do away with the hassle of crossing small lakes or seas that are only 2-4 tiles across vs crossing an ocean that is 6+ tiles across.