They are very similar, but here are some of the differences:
Theming and room decoration are different.
BC lobby restaurant has a character breakfast, while the YC lobby restaurant does not; as a result, the BC lobby is often more crowded and louder than the YC lobby.
BC store has a CS place to get sandwiches, breakfast items, etc.; there is no food in the YC store
Most YC rooms have full balconies; few BC rooms have full balconies.
BC is somewhat closer to Epcot; YC is somewhat closer to the DHS boat dock (although it is only a matter of a couple hundred yards in either case).
The resorts share buses to MK in the morning, but the buses stop at the YC first; on crowded mornings, it is not unheard of for a bus to get full at the YC, causing it either not to stop at BC or very few BC guests to be able to get on the bus; this can lead to longer wait times at the BC (overall, however, bus service is very good).
Portions of Illuminations can be seen from some lagoon view YC rooms; this is not the case for BC rooms.
None of these differences are major (except perhaps the balcony issue) and they are both wonderful resorts.