We run in to that same dilemma. There is no easy answer. What we end up doing is rotating trips (this one at BC, next one at CR, etc.). If I absolutely had to choose one resort, then it would be BC. I say this because our toddlers LOVE the pool. They sit and play in the sandy section for hours. We also do the character breakfast at Cape May quite often. But nothing can compare to being able to walk right in to Epcot each night. That is truly the deal-breaker for us. The kids go to various kidcot stations each night while DH and I enjoy some snacks or drinks from the relevant countries. It makes for such an easy, relaxing trip.
As far as the walk-though Epcot to get to the monorail.....we've done this several times. We always plan to do some rides in Epcot first and then just hop on the monorail to Epcot afterward. If we are in a hurry, then we just take the bus. On the way back to BC, we try to time it when our twins want to nap in the jogger, so we take the monorail back from MK to Epcot and walk through Epcot to BC as the twins nap in the jogger. It gives the kids a chance to rest and we adults can take our time, buy snacks, whatever we want. It works for us! But....as I said.....don't do this route unless you have extra time to spare.
