I'd say CR. We just returned from WL and while the hotel was great, we had difficulties with the transportation. Getting to MK isn't so bad, but anywhere else is very time consuming. One night, my son got sick at dinner at Poly and it took me over an hour to get him back to WL, bless his heart!!
Another night we took the monorail back from Epcot to TTC. We went to the busses and found out there no longer was a bus from TTC to WL. We had to get back on a different monorail, go to MK and then take a bus from there. ANother long trip.
With the kids, I'd do CR eventhough the theme may not be as fabulous as WL. (WL's theme is more for adults anyway. The kids still think CR is the coolest.)
We're planning on CR for our next venture.