Having recently stayed at both (the Poly in August of 2003, the GF this past February), I can say without hesitation that comparing the two resorts is useless. Their atmospheres are way too dissimilar; I love them both for very different reasons.
Both the GF and Polynesian have the best mousekeeping and best staff on property. From the woman who cleaned out my ashtra on the balcony every night (arranging a napkin into a Mickey head) to the gentleman in the GF who did our turndown service every night ("Will 6:15 be convenient for you for the rest of your stay, sir?"), both hotel staffs exceeded expectations.
I prefer the restaurant selection at the GF. Just my opinion. You'll find posters hwo are crazy about 'Ohanas. Since I prefer quiet, leisurely dinners and like to dawdle over wine and coffee, Citricos, Narcoosee's, and now the Grand Florididan Cafe address those needs - even though I love Kona Cafe.
I also prefer the lounges at the GF. Tambu Lounge at the Poly has always seemed like an afterthought - a bar shoved into what is in essence a second-floor waiting area. Mizner's Lounge, like the Belleview Lounge at the Boardwalk, is dark, elegant, and posh without being snooty (the beer selection, however, sucks).
The Polynesian is much more convenient however when travelling to Epcot. Walk to the TTC monorail. At the GF it can take almost an hour to get from the monorail station to the Epcot entrance if you miss the train.
There's my take!