After doing this in Sept with WL/AKL, I am planning to do this every trip now until I've stayed at least once in all the Deluxe resorts. This may mean moderate/deluxe split or a deluxe/deluxe split like we did last year.
I believe it adds to the experience, agreed there is some mild discomfort when the switching takes place, but none that would be bad enough to stop me doing it.
If I was with a large group or with children, my opinion may change but for Adult or Solo travellers, I would highly recommend this additional way of enjoying WDW!