I stayed in the village of Pontorson and caught the bus to Mont St Michel from outside Pontorson station. It went right across the causeway and stopped at the entrance to the Mont. There are also direct buses from Rennes station that stop there.
Despite the huge number of visitors the abbey appeared well organised with no congestion as visitors follow a set route from the nave through several chapels, the cloisters and crypts and back onto the steps again.