Allied ports

It's looks too strange to me, that your fleet can not enter allied port for repair. It is unlogical and unhistorical.

I agree and have thought the same before myself.

However I think the problem comes with what might happen if this was allowed: For e.g. an ally could innocently put a full naval stack in one of your ports thus depriving you totally of it's functionality in being able to build, repair and even offload/board troops in it.

A solution could be that the owning nation would just have priority and kick the ally's ships out with their own, similar to the way an army kicks out a hostile naval force, (but clearly on friendly terms here) and only kicking out enough ships to allow your given number access. So similar also to when you have a city will a full stack, but recruit more (excepting it's the ally's ships that are placed outside rather than the fresh units).