Someone said something about mixed reviews of the Polynesian. Most I've seen are from people who have never stayed there.
We love them both. We've stayed 30 times at the Polynesian and 6 times at the GF with another visit fast approaching.
Both have great service, theming and landscaping. Both have two pools.
The GF has more restaurants but we find it fun to travel by monorail to lunch or dinner so not a biggie for us although some of our favorites are at the GF. But Kona is at the Polynesian and a trip would not be complete without a meal or two there.
GF has a whirlpool if that matters to you.
The Polynesian has three beaches and no room is far from one. The GF has only one and it is not as convenient from many of the lodges. It also has the best view of Wishes and the Electrical WAter Parade IMO. Both are centered from the Polynesian.
Transportation from the Polynesian is the best on property. Monorail or launch to MK, walk to the TTC for monorail to Epcot....less walking then involved from the Epcot resorts to Future World. From the GF you must do the MK monorail circuit, walk the ramps and transfer. Both resorts have only buses to MGM and AK but that is why rental cars were invented. The TTC also has buses from AK and MGM so if you are bussing it, just catch the first that comes...TTC/MK or Polynesian. If you have a large stroller or a wheelchair, take the short walk to the TTC and catch the ferry to the MK.
The rooms at both are larger than the Epcot resorts but the newest buildings at the Polynesian are the largest standard rooms on property and make up around 40% of the resort. Tikiman reports them to be 476 sq ft! I can personally attest that they are very roomy indeed.
Both are wonderful resorts and I don't think you can go wrong. I would pick the theme that appeals to you most.