Don't get me wrong, I love the BC. It's probably my favorite resort and the pool is amazing. However, with the age of children, I think you are making the right choice for you. From BC, you either have to walk forever or take a bus to MK, which I imagine is the park you'll be spending the most time in. For those of us who spend most of our time at Epcot, it's great, but rather inconvenient for the MK travelers. And your children are probably too young to really appreciate StormAlongBay anyway.
Enjoy your stay at the Poly and when you are pushing that stroller onto the monorail and having such an easy transfer over to MK, remember that you made a great choice.