We stayed at Poly in Dec 2001 when DD was 9 months old, our next trip we had joined DVC and stayed at BCV in a one bedroom, no question about it, BCV all the way.
Poly is lovely, the monorail and great but the bennifits of BCV outway it by far. For one thing you will be doing a lot of walkig outside, where as most of BCV you can do inside or covered in the rain. Walking to Epcot is easier then taking the monorail to MK and often in the evening you end up at Epcot because the other parks are not open as late. Also there is the boat to MGM and the boardwalk and all the restants at S&D close by too.
Having said that SAB can not be beat for best places for 2 year olds. It was by far the best part of our entire trip. 2 year old DD loved that place. The sand bottom pool is amazing.
And while Poly is close to MK (and this is important) It is far away from everyother place. I thought the busses at BCV were fine. We even could see the MK fireworks at night from our 5th floor pool view 1 bedroom. We also love Beachs and Cream.
And this isn't even getting into how much better the accomdations at BCV are, I think that was covered already. You can save 100$ in food by staying at a villa with a young kid. It is so much eaiser.
BTW some people walk across Epcot and take the monorail from there, but I don't recomend this unless you do Epoct 1st then head out to MK.