The problem with naval AI is that I didn't have time to completely rewrite it before the release of the game, so while I've spent plenty of time on it between release and now, it's always been subject to a lot of bugs and tendencies for fixes to create more problems just by virtue of being very old code. This also leads to it having a lower priority simply because some tweaking here and there isn't ever going to make it great, and I rarely have the kind of consecutive free time on EU4 (I work on several other projects as well) that would be needed for a total rewrite + testing + inevitable bugfixes for the new system.
Wiz - a partial solution would be to make transports cheaper and not cost force limits. The AI seems to prioritize combat vessels over transport vessels (rightly, since if you can't protect your transports they're useless anyway) and just doesn't ever have enough of them.