I love, love, love the WL. I think the theming is great, I like the restaurants, and the grounds are lovely. I like taking the boat to the MK, and I enjoyed sitting on the balcony and watching all the comings and goings in the courtyard. I think the lobby is one of the most beautiful I've ever been in, anywhere in the world.
That said, you can't beat the Poly for location and, in my opinion, the relaxing atmosphere. The grounds are phenomenal. The garden views are great - even the ones that face the monorail. You can take boat or monorail to the MK and you can walk to the TTC (meaning you wait for only one monorail to Epcot). The rooms are also bigger, which is a key thing for us.
I think that if I really preferred one theme over the other, that would be the key to the decision. If you like both, and are visiting whichever hotel you don't pick to eat and look around, I'd say Poly wins for transportation options and room size.