We plan to take a train from Paris to Bayeux, rent a car and drive to MSM for one night and travel to Amboise the following day.
Option 1, return the car in Rennes and take a train to Amboise.
Option 2, drive to Tours to return the car, and on to Amboise.
This is our first trip to this part of France. Looking forward to your advice.
I really think a car is necessary for Bayeux to MSM. It's a short drive but you would probably be limited to whatever bus connections are available between the two, then limited again for when you have to connect to your next destination.
You could drop in Rennes. I'd check the train schedule. Tours to Amboise is a short jog and likely to have lots of local connections available through the day. Rennes to Amboise is likely more limited. If you have time, some stops on the way to Tours: Fountevraud Abbey, Chinon (a completely different type of castle), and Villandry (great chateau gardens).
When you reserve the car, be sure to Google map pickup and drop off locations to make sure they are convenient. If not, you might fing yourself getting to and from places that are far from where you hope to be. Bayeux is pretty small but Tours is big enough to have multiple rental agencies, some of which may be far from the train you want.
I was curious about the travel times involved, so I took a look at viamichelin.com for the driving times and sncf for the train times. It appears that you might save an hour or two by making the long drive to Tours, but I have no information on the driving conditions along the way. And there are other factors you might want to consider:
Trains from Tours to Amboise and from Rennes to Amboise are not terribly frequent, so you should check the schedules around the time of day you'd plan to hit the train station and see how long a wait you'd have if you just missed a train. Be sure to check the schedule for the correct day of the week if your anticipated travel date is too far in the future to check.
Last-minute tickets from Rennes to Amboise can cost up to 125€ one-way, so I think you'd want to buy early to snag one of the promo fares, but that would likely tie you to a specific departure time for at least some parts of the journey. There will be one or two connections required.
Tours is so close to Amboise that the walk-up rail fares may max out below 6€; in any case, they're cheap enough that you don't have to worry about the ticket cost. Some of the trains are Intercites (times don't vary by more than 3 minutes), and I don't know whether they require reservations (which would mean they could theoretically be sold out if you waited to buy your tickets until you arrived at the Tours RR station). I'm sure there are other posters who can clarify the reservation situation on Intercites trains.
Touraine Filvert runs buses from Tours to Amboise. They take 50 minutes vs. about 20 for the train, so they would be a distant second choice. There seem to be 6 or 7 afternoon departures on Monday-Saturday. I mention this only because the trains are sort of infrequent.
Consider taking the train from Paris to Caen instead. There are four rental agencies right across the street from the Caen train station. If you rent in Bayeux, the places are franchises far away from the train station with less selection.
I'd drive all the way to Amboise and drop off the car there. If you can't, then drive to the Tours TGV station at St Pierre des Corps, where there are many rental offices where you can drop it off.
Keep the same car for all the places you could possibly want a car, including all your chateaux visits. With the major rental agencies, it's no problem to pick up and drop off at their different locations within France. A one-day rental can sometimes cost as much as three days.
I have just returned from 4 weeks in France and the most disappointing element of the whole trip was Mont St Michel - the abbey was overrun with visitors and the rest of the Mont is full of tourist tat shops selling snow globes, fridge magnets etc and a few indifferent quality restaurants. It seems to be a long way out of the way if you are travelling from Bayeaux to Amboise. However, nearby St Malo and Dinard were interesting, but are further out of your way.