I'd say, without looking at it or having played it in a decade, Prime 3 could easily be remapped on a controller. It already used buttons to "activate" a lot of the motion prompts because you had to swap states so often in the game. And you have twice as many buttons as the Wiimote+Nunchuck setup.
I'm not sure that you can't do the game with the same control layout as the first two games have. You may need one extra button and the joycons have it. (And to be honest, the first two games could likely use an extra button too.)
The only motion control I remember that you'd really be missing, in terms of it sucks that you don't have it, is firing the grapple beam and yanking away shields. You can stick this on a button and it will work just fine but it wouldn't be as cool as physically ripping the things away from the guys. Especially if you're doing the lock-on hop and ripping from one dude while firing at another.