for us the deciding factor was the balcony. there are a few rooms at the bc with a full balcony, but most of the ones at the yc have one, and we knew, with young kids in tow, that we would be spending a lot of time out there while they slept (naps, early bedtime). it wasn't worth the luck of the draw at the bc. and for us, the extra couple of minutes to epcot wasn't really an issue, it really isn't that much further.
the yc rooms are very light and bright, not dark at all. we love the atmosphere in general at the yc, although the bc looks nice, too. I don't think you can go wrong with either choice. maybe make a list of what is important to you, or maybe make a pro/con list about each hotel and see if the cons of either of them makes a difference to you.
good luck with your decision!