I like MK on a rainy day. It clears the crowds out and there are plenty of shops to duck into and indoor attractions. Just make sure you have a change of shoes/socks and or water-compatible shoes because there are lots of puddles!
Of course, when we were there in September we spent so much rainy time in MK that it sort of stifled the magic. If you can go during a rainy time and a not-rainy time, too, I would recommend it!