If I disregard the fact that we're going gold (which favour the "no changes"), I would be in favour of changing the embarquement system because:
1) We could allow capture of embarked workers, which is something I really want.
2) Embarked units needing an escort to survive is bad for the AI.
So I would make embarked units not stack with naval units, but have a very good combat strength for defense, but cannot attack while embarked. (Can still attack while disembarking)
But that's a lot of changes. And will lead to "too many units for so few tiles" o'n sea, similarly to what we have on land.