The BC bus service does get the short end of the stick a little bit. Morning buses usually stop at the YC first. As a result, if there is a big crowd at the YC stop (which often happens for morning MK buses), that can fill up the bus, such that no or few BC people can get on the bus.
As for buses heading back, I have not seen the lines for the BC buses be especially long. These buses are usually shared with some or all of the other Epcot resorts, so there is no reason BC would be singled out in that regard. However, I do have a little bit of a trick to this: I always take the first bus that arrives that is going to any of the Epcot resorts. I then just get off that bus at the first stop and walk back to my resort (usually the YC). At MK, for example, there are two stops for the Epcot resort buses and they are right next to each other (I think one stop serves S/D/BW and the other serves YC/BC). I wait in the general area and whichever of those buses arrives first, I just take that one. It is then a short walk from the other Epcot resorts back to the YC. (I admit this may not work if you are leaving the park at a time when there are long lines at all the bus stops; otherwise, though, it works great in cutting down wait time for the buses.)
Overall, I think the WDW bus system is pretty good and BC bus service is good as a result.