Train from Munich to Lyon

That is an 8 hour train journey and you really don't have a scenic choice. Leave Munich at 9:02 am, with train changes at Karlsruhe and Strasbourg, and arrive Lyon at 5:03 pm. See for yourself.
https://int.bahn.de/en

I agree with the above-- it looks like the high-speed trains all take more or less the same route through Stuttgart, Karlsruhe and Strasbourg. This makes total sense, because you have to make it past the Black Forest, and this is the only high-speed rail line that runs in that general area and direction. If you really, really wanted to, and didn't mind adding several extra hours to your journey, you could stop in Stuttgart and transfer to the regional rail lines that run through the Black Forest, come out at Offenburg, and then travel on to Strasbourg and resume the original route. But, having traveled both routes multiple times, I would say that the Black Forest route isn't scenic enough to be worth the detour. If you wanted to do something nice along the way to break things up, there's a pleasant zoo right across the street from the Karlsruhe main station, or maybe there's something in Strasbourg near the station there. I would pick those stops over more time in a train, by a long shot.

For a not scenic choice I have taken many times the Regio Jet bus for exactly this route