The biggest difference we find (besides location) between the 2 resorts is that we tend to have more non-park things to do when staying at BC. At the BC, you can enjoy the boardwalk entertainment, movies and campfires each night, the surrey bike trail along the boardwalk, can walk to mini golf, Espn Club, ice cream treats at Beaches & Cream, etc. So if you plan to have a lot of resort time, the BC is a great option.
When we stay at BC, we plan lots of meals in Epcot. We also like knowing we can watch both Illuminations and Fantasmic and be just a walk away from our resort after the shows end and the crowds head for buses or boat. As far as getting to MK, if you have hoppers, one thing we personally enjoy is spending early morning in Epcot and then hopping on the monorail over to MK for a while. We have a double jogger and are not overly fond of taking a bus or car to the parks. We love walking, monorails, or boats.
When we stay at Poly, we plan lots of meals at the monorail resorts and also MK. We also tend to spend more time at MK than other parks. Maybe make your decision based on your park days and dining ADR's. Both are great resorts, really, you can't go wrong with either one.