I think a lot of it comes down to personal preference - theming wise we much prefer the light, airy nautical theming of Yacht and Beach Club to the dark, wooden architecture at the Polynesian.
The pool at Yacht Club is IMO hands down the best on Disney property. We used it every day and the set up was fantastic - steps away from the room, with Beaches and Cream seconds away if you want to grab some ice cream and Hurricane Hanna’s very close too if you’d like something more filling. There’s so much at the pool to occupy the whole family - I personally opt for Yacht Club for the pool alone! Plus, swimming while watching the Epcot fireworks go off is a pretty incredible experience.
We also loved the close proximity to Epcot and DHS, however the Polynesian’s location right on the monorail is also invaluable if you’re planning on spending a lot of time at Magic Kingdom.
I also think it’s worth taking into account which restaurants you’d like to eat at - both hotels are close to lots of amazing options.
I agree that I’d stick to one hotel for the three nights - the hassle of moving would for me exceed any gains from being closer to MK for the last night.
For me, I’d ask these questions when deciding:
1) Look at photos of each resort, communal areas, rooms, etc. Which do you prefer stylistically/ practicality wise?
2) Would you prefer to stay near to Epcot/ DHS or MK? Think about your breakfast/ dinner plans and which resort would tie in best with those.
3) Which restaurants are you mainly focusing on? It’s pretty quick getting to walk to your dinner at Epcot or the Boardwalk if staying at Yacht Club, but if you’re eating much more in the MK area, the Poly might be more convenient.
