We enjoy doing split stays if we are staying awhile - it's not worth it to pack up everything after just 2 nights IMO but if you're staying longer than that, it's fun to have a change of scenery and location.
It has not been a pain for us, really, but we are all adults. We did one trip (last year) were we stayed no more than 2 nights anyplace, and that WAS a pain. But our last trip, we stayed a few nights with my mom and then moved to WL.
Great thing about Disney resorts is that they will move your luggage for you, so you just hop to the other resort to check in and go on your merry way. I think splitting is a great thing to do if you want to be close to the parks you are spending time at - stay at an Epcot/MGM resort for half, then a MK resort hte other half. YC and WL would do that for you =)
We adored WL, and i think YC is just gorgeous with an incredible pool. Good luck deciding!