Route suggestions?

Depending on what part of Canada you are at, it generally not recommended to get in a car immediately. While the area around Bayeaux is easy driving, the first part getting out of Paris, especially at rush hour can be more tasking. (Made the mistake once of flying in from London and picking up at 5 pm on a Friday. Horrible traffic!)

I would be flying from Toronto, ON and I don’t want to drive around France at all so I would be travelling by train. I’m just looking for the most efficient route I guess beginning with Paris, Bayeux - beaches/ Mont St Michel, Lyon (July 3-8), Arles, Avignon, Nice … I know there will be some back tracking but I wanted to avoid as much as I could and travel by train (bus if needed)…

The most efficient train route would almost certainly be through Paris, involving a change of stations. This website can help you look for train routes (use "Aeroport Paris Charles de Gaulle" for CDG), but I doubt if you'll find a way to bypass Paris.

There is TGV (fast train) service between CDG and Lyon that keeps you out of Paris. If your dates are still flexible around the Lyon conference, you might consider that option right after you land or right before you fly home (but with an ample cushion so you don't risk missing the flight). You might also look for a TGV that takes you between CDG and Avignon or Nice (probably via Lyon?).

You definitely can't avoid going through Paris between CDG and Bayeux. If you can't avoid Paris between Bayeux and Lyon, you might consider breaking up your Paris time into two segments, maybe with hotels in different neighborhoods.

I don't know how long your total trip will be, but Amboise is in the Loire Valley, closer to Bayeux than the southern cities you mentioned. It has train service to Paris, maybe also to Bayeux. Spend some time with a map and the DB site above.

Some good comments already.
I will just add that it is unfortunately not practical/feasible to use Bayeux as a base for Mont Saint Michel if you do not have a car. And even if you do, you might regret it as you will spend your time on the Mont with scores of daytrippers.
Plus, with only four nights before your conference in Lyon you have to pick ONE between the Mont Saint Michel area and Bayeux/DDay beaches. My choice goes to Mont Saint Michel, but this is very personal.
You would then spend 1-2 nights in your area of choice, and 2-3 in Paris. It is very quick, and you might as well spend 4 n in Paris. There is so much to do and daytrip options abound.

Also, after Lyon: do you need to go to Amboise? You will backtrack a lot to then go to Avignon, basically losing a day of travel each way. I would skip it.

Is it possible to take a tour from Bayeux to Mont St Michel?
I was hoping to go to Amboise as I wanted to see Chenonceau but I might consider skipping… conference dates aren’t flexible but depending on the agenda each day I might be able to skip and do a day trip somewhere near Lyon. I appreciate all the great feedback! This will be my first time in France and I wanted to kind of ‘see the heart’ of it :)

You're leaving Toronto June 28, arriving CDG June 29, you have to be in Lyon four days later on July 3. Hopefully the conference will provide enough free time to see some sights in Lyon, but you can leave there July 8. What's your return date to Toronto? How much time do you really have to see "the heart of it"? Keep in mind that each day you move between cities is wholly or partly lost for sightseeing -- pack, check out, to the station, ride the train, to the next hotel, etc. The ideas you'll get here will vary a lot, depending on whether your homeward flight departs, for example, on July 12 or July 22. If you haven't lined up the flights yet (and ten months out would be earlier than you have to), try to give yourself as much time in France as you can.

I agree with the comment about Bayeux and MSM. Googling "day trip to mont st michel from bayeux" produces a lot of links, and I have no experience with any of those tours. It would be a long day and a short time at the Mont with a lot of other people, but a good guide could make it worthwhile. Otherwise, getting to MSM by rail and bus would eat up too much of your day.

Paris alone would be worth a week on a first visit, or more. If you're there July 14 and (please God) the pandemic has receded, you could enjoy the Bastille Day celebrations.

So I haven’t yet booked flights I’m going to try to return home to Canada on July 16/17… I was hoping to see highlights of the ‘heart’ of France - I know there’s lots of time spent checking in/out, trains, etc… I will continue to check out tours for MSM and see if it’s manageable to do both MSM and DDay beaches somehow without losing a ton of time. Thanks for all your great suggestions!!

Hi Kmander2, I am also trying to see MSM by public transit combined with time in Bayeux and Paris next summer. In my search on this forum, other travelers shared that The Winston Churchill hotel offers a daily shuttle bus to Mont Saint-Michel from the town centre of Bayeux (about $50 or $60)? Of course you’d be at MSM during peak time with other tourists, but sometimes that’s the only option on a tight schedule. I don’t think you have to stay at the hotel to take the shuttle but they may offer a better price if you do. Lucky you to attend a conference in Lyon!
(PS my time in Avignon and Nice in early July 2018 was super hot. Pack your sunhat and light summer clothes!).

It sounds as if you have about 3 weeks to discover France! If you haven’t booked flights, it might make sense to leave July 1-2 and go directly from CDG to Lyon for your conference. You could then continue on south to Nice. Then, head north stopping at Avignon and transiting Paris to get to Bayeaux. Finally head back to Paris for remaining time - you could get to Amboiise on a day trip from Paris. If your schedule permits, this itinerary might have less backtracking and only 1 transit of Paris.