We have split several stays, but always because we could not get the hotel we wanted for the whole time. We once split a 6 night (3 at ASMU, 3 at Contemporary) because we were booking just a couple of days before we wanted to arrive. We split a 3 night stays (1 at ASMu, 2 at CSR) because we wanted to stay with friends at CSR and did not book until just prior to their coming. And we once split a 2 night stay (1 at POFQ and 1 at AKL) because we were altering the booking late. It was not much of a hassle for us, but we went into it with no expectation of entering a park the morning of the switch. Since you are talking about the AKL I will tell you what we did when we split with POFQ and AKL. It was December 2002. We had tickets for Mickey's Very Merry Christmas Party. Our plan was to arrive Saturday am and go to the Animal Kingdom, then check into the AKL around 3, and make our way to the Magic Kingdom for
MVMCP. However, our tickets were really for Friday night, and I had made a mistake with the booking. We could not get another night at AKL so I took POFQ, which is a very nice resort. We arrived at POFQ Friday afternoon and spent very little time there before going to MVMCP. We slept in Saturday, as we were tired from being out late the night before, had a nice breakfast at the food court, and then packed up and moved to AKL around 11am. Our room was not ready, so we spent a couple of hours in the Animal Kingdom, and then enjoyed the resort (which has tons of porches and viewing areas. We had dinner reservations at Boma that night, so when our room was ready, we just had our luggage delivered to the room, got ready for dinner and went downstairs to Boma. After dinner we went to MGM to watch the festival of lights. On Sunday we at breakfast at Boma, checked out and went to Epcot. It was a great weekend. It sounds hectic, but it actually was kind of relaxing to not spend a lot of time in the parks on Saturday and enjoy just hangin out together.
I guess the short moral to my long story is....don't be scared to split a short stay, just understand that your day will be somewhat wrapped up in the move.
PS - my kids are currently 3.5 and 7