I love both! Stayed at both, and here is my rundown:
Decor:
I prefer Polynesian. I like the dark woods, huge rooms, flat screen TV's, large bathrooms, the beautiful grounds.
BWI is due for a renovation (which it is starting this summer, apparently), and I found the rooms a bit to pastel for my tastes. But that's me.
Staff:
The staff at BWI was amazingly friendly and helpful.
I found the desk staff at Poly to be below my expectations.
BWI FTW on this one.
Food:
Poly has a 24 hour snack shop, which was important to us, who are night owls. We were so-so on Kona Cafe, and had to cancel our 'Ohana ressies. Did NOT like the luau (but that isn't a "drop by and have dinner" place anyway)
BWI has many many options during regular meal hours, including Spoodles. Flying Fish, ESPN, and Big River Grille. Lots of options. But their only 24 hour food is room service, which is expensive and, at least when we went, limited and not good bang for your buck.
Winner here depends on what time of day/how you like to plan your meals.
Transportation:
You can't beat the monorail to the MK at Poly. It was amazing. And being able to walk to the TTC to get to ride to Epcot was double plus good. Bus service seemed fine, and only shared with the monorail resorts.
That said, we love World Showcase, and getting to walk there from the BWI was fantastic. We are so looking forward to that again this year when we return to the BW--we felt we didn't get enough time in World Showcase last trip (though we got tons of MK time!), because it was such a pill to get there--walk to the TTC, take the monorail, then the long walk across Epcot to get to WS, and reverse it all to get home.
Oh and don't forget the quick boat ride to DHS, too.
We did find the buses a little tedious at BWI, since we had stops at Swolphin and Bacht Club before going to DTD and MK. But it was never too overcrowded, as some resorts complain about.
We opted for BWI this trip because half the trip there will be
MVMCP going on at MK, so the bonus of having the monorail to get to MK is lessened since most nights we won't be able to go to MK. So BWI it was on this alone.
Hope that helps you with your decision!