I realize this was posted like a decade ago, but I hope they don't do this, and honestly I don't expect them to. Hopefully they'll be smart enough to let every game work on every Switch. The console already has a precedent of playing all of it's games at different spec caps depending on whether you're playing handheld or docked. All they'd have to do is add a third mode, which plays games with higher resolution, quicker load times, etc if you're playing on Super Switch.
I can see a few Switch Pro exclusives but I don't expect there to be many. I'm thinking they'll be about as big as the DSi or New 3DS libraries. So about 6 games max, lol.