Well the fastest route is an overnight train from Lyon south to the coast; along the coast and north to Milan; then east to Venice. It can be done as an overnight journey in around 8.5 hours.
So you do have the choice of a fast route or ignoring 'efficiency' and not so much picking a different route, as making a different plan of where you want to spend your time.
You could actually look at parts of 3 of the most 'scenic' train routes to consider in crossing Switzerland. The Golden Pass line from Montreux to Lucerne; the Glacier Express from Zermatt to St. Moritz; the Bernina Express from Chur to Tirano.
By connecting from the Golden Pass in Brienz to Visp on a 'normal' train and then riding on the Glacier Express to connect with the Bernina Express in Chur, you could actually ride all 3 of them in part. I have no idea how the scheduling would work out though. It would take a bit of timetable checking obviously.
Since you are considering an alternative to the most 'efficient' route from Lyon to Venice, my question would be why you have chosen to concentrate on only the Bernina Express? Then, if you want to stop in Switzerland, what do you want to see and do in Switzerland other than see the scenery from the train? If the idea is mainly about trying to maximize the scenery on the route, then looking at the 3 express trains above, you could try and pick out the most scenic sections to combine.
Regarding Chur, I disagree with Pauline's memory while acknowledging that we all like different things of course. Chur actually does appeal to a lot of visitors. Perhaps the memory has more to do with just being in the area of the train station rather than having spent any time wandering around.
One of the best sites for info on Switzerland is the MySwitzerland site. Here is there take on Chur. http://www.myswitzerland.com/en-ca/chur-the-alpine-city.html
Obviously, there are also numerous other places you could choose to stop between Geneva (where you would likely enter Switzerland coming from Lyon) and Torino.
My wife and I are like Pauline, fans of Davos. In fact, it is one of our favourite areas in Switzerland even after having spent a total of perhaps a couple of years in Switzerland visiting for varying periods of time in pretty much every region of the country. Our last visit to Davos, was just last September. We do not stay in the city itself but in Wiessen, a small village just up the valley.
My only question in regards to where you would stop, is that while an overnight enroute to Torino could be spent almost anywhere, if you chose to spend more time, then the choice of where to stop changes based on what you would do with your time there. Chur for a day would be fine, but for 3-4 days, perhaps not. Davos (or lots of other places enroute) could have enough to interest you for much longer.
I think I am back to do you just want a nice scenic ride across Switzerland with an overnight somewhere along the way or do you actually want to spend some time in Switzerland. ie. several days.
Re the 'scenic' trains. I often wonder if they are worth bothering with compared to 'normal' trains. Yes they do have a few perks like roof windows and dining cars etc. but even riding 2nd class in the 'local' trains that stop at every stop are SWISS trains. What I mean is that NO seat on any Swiss train is not going to give you the same views and pretty much the same comfort. While local trains stop more often, you can also pick 'IC' (InterCity) trains which are just as fast as the 'scenic' (and Express) trains and cost no more for a 2nd class ticket than the slow trains do. So I do question where the value for money is in the Bernina, Glacier and Golden trains.
Riding 'normal' trains gives you incredible time flexibility in Switzerland. There are very few times if any you could ever be more than an hour between connections from/to anywhere. Often, when changing trains on a route, you have a 2-10 minute connection time and yup, they are that on time that making a literally 2 minute connection is the norm and as simple as stepping off the train on one track and walking across the width of the platform to get on your next train, on the other track. The 'scenic' trains do not run as often obviously as normal trains and so you are more limited in flexibility.