I wouldn't worry about the change - if you can book it! Disney will transfer bags for you and you'll just have to check out of your first hotel and pick up key cards at your second one. Really no hassle at all. I wouldn't do it for a short stay, as you would want to concentrate on parks, but for multiple weeks, a change of scenery isnt a bad idea. You really wouldn't even need a rental car, you could use disney transport and hotel transfers, and just grab a cab for your universal days.
Three weeks is a very long stay... if there is such a thing as too much Disney, I think you are about to find out. Would you consider doing a couple of weeks at Disney and then visiting somewhere else for your other week?
As for order, spend your two weeks first in the hotel that really excites you, and then try the other as a change of pace. AKL would probably be your children's second choice, and you could always book a meal at the boardwalk hotels to get a taste of them too. Or, slide down to a mod and save some money for the souvenirs. Coronado is nice and makes for a 5 minute trip to the waterpark, if your kids are into that.
Have a great trip!