I like the Prime games, overall, better than any of the 2D. I don't think the 2D games' gameplay aged as well and that most of the gameplay mechanics of 2D sidescrollers in general are antiquated. Not to say that they can't be good in the modern era, but it's definitely difficult, and I believe that the games require a degree of nostalgia to appreciate.
For instance, I didn't play much of any of the 2D Metroids, outside of about half of Fusion, before the Prime games. I didn't play Castlevania at all. I DID grow up playing Commander Keen, which to a degree shares some similar gameplay mechanics. To this day, I don't really enjoy Castlevania, I can tolerate the 2D Metroids, but I love replaying Commander Keen. It's a nostalgia thing.
I love the Prime games though, and I personally prefer Prime 3 above the others. I do like Prime more than Prime 2, though. I think Prime 3 had easily the best polished gameplay, the best visuals, and the best puzzles - it just needed a traditional control scheme to be available for those that didn't want Wiimote motion.
I'm pretty confident that the Switch port, when we eventually get it, will have that, though, and many of its detractors will learn of its superiority.