I love both - they are my favourites, but the price difference is huge. I have stayed at WL most - for the price and theming. This time i am staying at the poly for the theming and convenience.
The main differences to me are as follows - Poly feels like i am somewhere tropical - the lodge feels like i'm in the wilderness - love both themes.
Both resorts are relaxing - poly rooms are better as they are larger - but WL rooms can be better for younger kids who like bunkbeds.
Poly roomservice wins hands down - much more choice and more luxurious. WL pool area - prefer this because it has hot tubs.
Recreational options - good at both.
Transportation - both are good, but the poly can't be beaten on a short trip, for the monorail.
Restaurants - both v similar qualities of restaurants but i believe WL doesn't have the character breakfast anymore. As for the counter service ones - I don't like either a lot - but the poly wins as it is open 24 hours.
Childcare - both are good - but the poly is by far the best themed and most exciting for kids - neverland club.
Friendliness of CM's - all seemed extra friendly at both resorts.
Is poly worth the extra? Well, i prefer it on a short trip, as i don't notice the price difference so much over 3 or 4 days. But sometimes i have stayed 14 nights - and i certainly would have felt the price difference if i were paying for the poly as opposed to the lodge.