Both of the superbike championships are conducted on tuned versions of publicly available bikes whereas MotoGP are purpose built. Currently they all use similar engine configurations (size/stroke/cylinders etc..), but this has not always been the case. BMW have not been on the scene long since they didn't really have a suitable model until they released the S1000RR, so I guess they don't have much appetite for a completely bespoke model to compete in MotoGP.
The MotoGP bikes are slightly quicker, but not by much, I think 2-3 seconds is usually quoted. The main difference is the race format as the superbike events are usually conducted with 2 or 3 races over the weekend.
Finally, the WSBK and MotoGP are conducted on tracks all over the world, but the BSB is mostly confined to British tracks with the odd one at a neighbouring country.
EDIT: took too long writing this and didn't notice the other replies! Sorry