I've stayed at the Beach Club, Saratoga Springs, and the Poly and my favorite by far is the Beach Club. It think it does depend on what you are planning on doing during your vacation. We are huge pool people, so Storm Along Bay at the BC cannot be beat. We also loved the decor, the bed linens (sounds strange I know...but I want fluffy, white cotton linens, not polyester comforters), and the staff. The location is amazing, too, as EPCOT is our favorite. We do spend quite a bit of time at MK with our four and a half year old, but didn't have any bus problems. We usually go to MK for rope drop and hop in and out of EPCOT. Also, the whole Boardwalk area is just incredibly lovely.
Saratoga Springs was lovely, but very large and spread out, being a
DVC resort.
I was so excited to try the Poly and was thrilled about staying on the monorail, but I was so let down. The pool is tiny, the rooms need a serious update as a lot of the furniture is worn out/scratched, etc and we didn't think the CMs were anything special. Of course, a lot of people love the Poly.
The Contemporary is beautiful and a real Disney icon in my opinion and I'd love to stay there someday, but its really expensive and we're super happy with the Beach Club.
That said, we are doing a split stay in July with the first four days at the Beach Club and our last three at Animal Kingdom Lodge, where I've always wanted to stay. You really feel transported to another world out there, but it is a bit remote when using Disney transportation.