In a nutshell:
- Theming. One lends itself to the Polynesian islands, the other lends itself to Victorian-era American beach resorts. I recommend looking at photographs and videos of both grounds to see if one appeals to you more than the other does, as you might enjoy your stay there more. For example: the lava pool at the Polynesian is a lot of fun, but the Grand Floridian has an exquisite lobby and turn-down service in all of the guest rooms.
- Food. Your dining options are extremely different between the two. While you can obviously book a meal at any restaurant, it might be worth looking over the menus at the dining locations at both resorts, particularly at the QS locations. The Grand Floridian has more dining options in general, but I love the food at the Polynesian Resort, which is also home to my favorite bar, Trader Sam's.
- Shopping. This isn't important to some people, but it's worth noting that the Grand Floridian has more shopping options than the Polynesian Village Resort.
- Spa services. The Grand Floridian has a spa (I think multiple spas, but someone feel free to correct me if I'm wrong!) on property if that's important to you.
As far as
transportation goes, which is normally something I look at when comparing two resorts, the two are similar enough. The only thing that is a little annoying is getting to Epcot from the Grand Floridian. You can walk to the TTC from the Poly, which will take you to Epcot via monorail. In theory, you can walk to the Poly from GF and then from the Poly to the TTC, but I think I would rather just get on the monorail from the GF to the TTC and transfer.
Unless there is a marginal cost difference between staying at the two resorts, I'm more inclined to recommend the Grand Floridian. We love the Poly (our DVC home!) but there's something extremely "magical" about the Grand Floridian to me. I would definitely look at both and see which one appeals more to you/your travel party!