It's a tough balancing game.
I've seen some stupid AI embarkations. Like, playing a OCC with a one tile pass at one side, the AI there declares war on me. What does he do? Sends one infantry to get picked off by my artillery. Continues sending one unit at a time. He gets tired of that. What does he do? Starts sending embarked units, one at a time, to try to go around me. Well, geez, sounds great, except my destroyer there is pretty good at picking off unaccompanied units. And if not, my city and artillery from the land are pretty good at bombarding. It's true, he did get a couple through, but when you're talking a 2HP unit, my infantry back are pretty good at picking them off.
They try to use it too much. And I still think it would have been better in the game had embarked units been like civilian ones, so you can stack destroyers on top of them to escort them. But overall, I do in some sense like the idea. In theory, it will be easier for the AI, since they don't have to worry about getting the exact mix of boats correct. It will take some work and some refining - honestly, I don't expect much from this iteration, not because of the issues that everyone thinks, but just because it will take time to figure out the algorithms. But in the long run, it will make sense for the series.