It is really up to you.
You suggested that each ship types other than transport should be able to carry up to one regiment. I think this would be interesting, because in old days (and I assume it is still a practice), the ships typically had a detachment from their country's marine corps (or an equivalent) which served as both a protection for officers against a mutiny and a fighting force that can attack and capture places on the coast.
Ideally, such a small landing force could be used to immediately seize islands and isolated possessions of an enemy, as the British has been prone to do in 18th and 19th centuries. It would not be advisable, however, to land them in an area where enemy has a small forces there, even if it's just a mere 2k in size (or can 1k still defeat 2k with higher morale and discipline? I wonder...). The way EU4 currently works means large armies can still be sent overseas... in other words, quantity seem to be more important than quality in this game, unfortunately.