Hubby and I have stayed at both: BWI in 2004, and Poly in 2007. We love both for different reasons.
POLY THOUGHTS: We loved the decor at Poly--we prefer the dark woods and exotic grounds. We loved loved loved having the monorail right at our resort. Having Magic Kingdom so close, to be able to just "dash off" at a moment's notice, was fantastic. Also having the TTC within walking distance was another bonus, so Epcot was never far away. Lastly, having both Contemporary and Grand Floridian on a monorail hop away meant our restaurant, bar, and resort shopping/entertainment options were tripled at least.
The rooms are HUGE. The beach is a fun novelty. Having the rooms divided up into buildings, and having entrances/exits at both ends of each building means you can head right off in whatever direction you want and not feel like you had to hike around a loop to get where you wanted to go. We also had a second floor room in Tokelau which had a big balcony overlooking the quiet pool. That was a real treat, especially when torrential afternoon rains (Sept) would invariably hit, and we could sit out there and watch and listen to it pound down--novel for us Seattlites, where people think it rains a lot, but never like THAT!
BOARDWALK THOUGHTS: World Showcase is one of our favorite places in The World...maybe THE favorite place (though we love the rides at MK

, so having that in our "back yard" was fantastic. Just being able to walk over to get a drink or grab a bite to eat or see street entertainment...priceless. And that doesn't even take into account all the stuff already AT the Boardwalk!
The boat to MGM/DHS was novel, but not as quick as we would like, and the boats leaving were often packed, but we were too tired to walk the distance back to BWI, so we would end up waiting a long time or give up and take a bus to some other place directly from DHS instead.
We don't like the decor at BWI as much, and felt the walk from the elevators was long--having the elevators so centralized means a long walk when we were roomed at the end of the hall. For instance, to get to WS, which we always wanted to

, we had to hike all the way down the long hallway, through the lobby, out and down the stairs, then loop back the way we came along the long walk off the property... At the end of a long day, or with sore tired feet from a week of walking, those distances felt really far. We are requesting a room closer to the elevators this time, though we may regret it since the soundproofing between the rooms and hallways was not that stellar and rowdy kids in the early morning parading past are hard for these night owls to take! Of course, now that Adventurer's Club is closed, we might not be out so late. Though there is always Jellyrolls, which is right ON the Boardwalk. We never did get to try it when we were there last...
So at any rate, both are really top notch resorts. We are staying at the BWI on our next trip in December. We wanted to be close to World Showcase this trip, and it works out because almost every other night we are there,
MVMCP will be on at MK; so had we chosen Poly, the novelty of having Magic Kingdom so close by would not have been able to be enjoyed like we did on our last trip. But I think we prefer Poly by a thin margin over BWI, but very thin.
I hope this helps!
(PS I know you said you stayed at BWI, and know its amenities, but wanted to enumerate for others who may not know)
Jackemail, I see you booked a split stay for next year. We also were at Boardwalk Inn all last week and booked the BWI for next year! We never thought of a split stay......and hubby has been intrigued with Poly, but we really loved the location and convenience and entertainment at BWI? Can you tell me which is your favorite? POLY or BWI and whY? I have read that some of the rooms at Poly are in need of renovation? Where was your room at BWI?