Our favourite WDW resort is Wilderness Lodge. It is just so breathtaking and awe-inspiring. You can't help but be impressed by the large lobby. A lot of people complain that the rooms are dark (dark furniture and accessories) but we absolutely loved it. We loved being able to hear the music from the Electrical Water Pageant while sitting on our balcony in the evening, being able to watch it from the beach, the boat to MK, the opportunity to be flag family, the Hidden Mickey hunt - just everything!
A very close second is Boardwalk Villas (or Inn) - it's all about location, location, location! We love being able to walk to Epcot and Hollywood Studios. You can't beat the convenience of the International Gateway - after Illuminations have finished and all the crowds are slowly pushing their way to the front of the park and fighting for buses or monorails, you can take a slow stroll out of the IG exit and back to the hotel. The Belle Vue lounge is the most relaxing place to have a pre-dinner drink while sitting in the sunshine and watching the world go by and, for me, you can't beat the atmosphere of an evening spent on the Boardwalk, strolling around the lake and enjoying the entertainment.
Just one thing to note - have you booked with the free dining plan? If so, I'm not entirely sure you can do a split stay. If not, then go for it. We love split stays!