I wouldn't worry to much about it being busy where ever you go. Sept. is way different than July or early Aug., and by late Sept there is hardly anyone around.
I would say your odds of encountering unpleasant winds on Pine are pretty high. For whatever reason I've never loved Pine, and much prefer the Pikes, but Pine does let you visit the Falls. You can get into Pine with zero portaging. In the eastern area, generally North-South portages are going to be harder, East-West easier, besides the very short N/S.
How far do you want to paddle? Clearwater-Mountain-Moose-Fowls-Royal River-John-Pikes-Clearwater is and awesome loop. Good fishing too, maybe not as good as Zac's top secret lake trout lake, but good.
Quinn