The one big draw of YC/BC for the hot month of September is Storm Along Bay. If your children are huge pool fans, then YC/BC becomes a strong contender and top choice. If you are primarily looking at the MK/Epcot then the CR is the optimum choice. As a hotel, I find the theming just as good at the CR as at the BC. Also at the CR the rooms are bigger/more comfortable, all tower rooms have a balcony, the walkway to the MK is priceless and the access to other resorts is best of all the WDW resorts. If walking inside the hotel is an issue, the halls are long and convoluted at the YC/BC whereas e everything is very close at the CR. The BC has the Marketplace for quick service, but the Contempo cafe at the CR is leaps and bounds better, IMO. Both resorts are near other resorts fro lots of dining choices, but we find the dining in the MK area resorts to be more to our taste than the dining in the Epcot resorts. However, you do have all of World Showcase at your doorstep at the BC!
Personally, I would choose the CR, but that is MY personal preference between the hotels. Lots of people would prefer the BC with its great pool and easy access to both Epcot and DHS.
Good luck choosing!