Just an idea but I do not like harbours holding thousands of units. All harbours have a size limitation therefore I propose Grepo harbours should be limited too. Should make attacking and defending more challenging.
While super-stacks can be a complete pain, I don't think it makes sense to limit them.
The harbour itself may not be of limitless size, but the number of ships you can build in that harbour is limited by the farm space in that city anyways.
Think of it more like a standing blockade. The defending ships are all scattered around the ocean next to the city. They aren't all crammed inside the harbour.
By the way, you need to format your idea before Figgy spots that you haven't.