I have two options to visit Mont St Michel...first is to take a day trip from Paris (approx 13 hours including travel) or take a short trip from Bayeux using Churchill Hotel shuttel that only allows three hours to visit. (is that enough time?) I dont want to rent a car. Which would be the better option?
Both will present MSM in a very poor light and you will go home telling people how crowded it was and less impressive than you thought it would be.
Of the two options you list, the trip from Bayeux would be better only because you will spend less time stuck in a bus.
However, if you could somehow get yourself to MSM at 5PM and stay overnight and leave at 10AM the next morning, you will find it absolutely magical (but pack some food since the restaurants are famously bad).
Agree that option two is better, but neither is ideal. Three hours is probably enough time to walk up the winding road to the abbey, wait in the line for mid-day admission, tour the abbey, then walk back down. Don't expect any time to explore the ramparts, though.
There is one good restaurant on the island, Restaurant St. Michel. All the others are owned by the same company and serve an identical, not particularly memorable menu.