I have stayed at both and really enjoyed both, but my favorite is the WL.
Things I love about the WL
1. Everything is covered. When it rains, you can take the bus at the WL and from the moment you get off the bus until you are at your room, you are either covered or indoors.
2. It is significantly less $ than the Poly,
3. The geyser and hot tubs.
4. The convenient short boat ride to Hoop Dee Doo. One of my favorites.
5. The absolute friendliest staff of all the resorts I have visited.
6. The yummy cupcakes, salads and sandwiches at Roaring Forks.
Things I loved about the Poly.
1. Transportation options and convenience. Like previous folks mentioned, it is a short walk to the transportation and ticket center to catch the monorail to Epcot.
2. I believe it has the largest square footage rooms and I really like the daybed/sofa.
3. You can get dole whips from Captain Cooks.
4. Breakfast at Kona Cafe... YUMMMMY
You really cannot go wrong with either one. I think the counter service options in both Roaring Forks and Captain Hooks are great, so I wouldn't worry too much about the food court issue.
I hope you enjoy whichever one you choose.