We just did a split stay and it worked beautifully. We did it for the same reasons as you, I couldn't decide on a resort and I'm not sure when we'll have a chance to go back. We did BWI for 4 nights, GF for 3 nights, AKL for 2 nights, then back to the BWI for 2 nights. We planned it so that we were in the parks closest to the resort on the same we were there. All three times that we had luggage transferred we encountered no problems at all. The luggage was always waiting for us even when we left at the same time.
For example:
Sat 1st day - BWI: Arrived; cruised the boardwalk
Sun 2nd day - BWI: DTD / Epcot
Mon 3rd day - BWI: Blizzard Beach
Tues 4th day - BWI: MGM
Wed 5th day - GF: MGM in the morning; lunch at Epcot; transfer to GF. We had a nice dinner at Narcoosee's then went to watch Spectro and Wishes.
Thurs 6th day - GF: AK in the morning; MK in the afternoon
Fri 7th day - GF: MK all day
Sat 8th day - AKL: MK in the morning; check out and move to AKL. AK in the afternoon / evening.
Sun 9th day - AKL: AK all day
Mon 10th day - BWI: Slept in; late breakfast at Boma; wandered around the hotel, transferred to BWI. We caught the bus straight to Epcot and had luggage transferred.
Tues 11th day - BWI: MGM morning; Epcot at night.
I know most people don't like transfering, for us it was no problem. When we were going to the AKL for just the 2 nights, I packed everything we'd need into one suitcase and stored the others in the closet. I'm so glad we got to experience so many great hotels; I wouldn't have changed a thing about our trip.