I say go for it! - We did our first split stay last December and
loved it. (We did POFQ, then left property to spend Christmas with family, then did AKL.
Click here -> Mini Trip Report)
If I were able to do 16 nights and wasn't sure when I'd be back, I'd choose:
An MK resort - Poly & GF are on my wish list, but CR is
super convenient if you like the style
An Epcot Resort - I haven't done YC or BC yet, so listen to the others! (Epcot & DHS)
Universal - Hard Rock or Royal Pacific, depending on which appeals to you
then end at AKL (AK & Disney Springs)
This allows you to use Magical Express from/to the airport on both ends and also solves the 14 day problem, because Disney will consider it two different trips. - You should be able to book ADRs and FP+ for each when you hit the separate windows.
As far as the order I chose, It allows for the magic of MK to open the trip, and saves the special request of AKL for the end so there's always something to look forward to. (
But, if snagging a great time for FOP at AK is a must,
you could switch your Epcot resort and AKL, so AK will be later in your window.)
As for how many days at each, I'm torn between 4 nights at each or 4/5/3/4. I guess it depends on whether you want to do Volcano Bay at Universal?
You'll obviously need to move on your own for the Universal portion of your trip, but you can use a taxi/Uber or rent a car from the Disney Car Care Center. (They'll pick you up at the resort you're leaving and take you to the CCC to do the paperwork, then when you return it, they'll take you over to your new resort.)
Group your park days according to where you're staying, and make sure you leave some down time at each resort as well -
especially AKL!!
P.S. - Pack one of those hanging shoe bags for your toiletries and stuff. That way you can just fold it over into a suitcase each time you move and hang it right back up in the new place!