I think both 3D and 2D Metroids has its cons and pros. Tbh, I think that both can and should coexist, and that's the same way I feel about franchises like Zelda. I hope that Nintendo can bring us Metroid 5, and not just bring us Metroid Prime 4. I must say that I'm definitely more hyped about a new 2D Metroid than a new Prime, because it's been a long time since we didn't have a pretty good 2D Metroid.
About Samus Returns, I haven't had the opportunity to play the game (sadly, I sold my 3DS a while ago, and I still regret that choice, but it's late now ). But I heard that there are teleportation rooms in the game? I mean, that doesn't make the game feel more linear? It's what kept me worried about it. I mean, Metroid games is about backtracking and find new paths with your new adquired power-ups. Also, how does the 3D feels in this game? I'm about to buy it with a friend who still has the 3DS, and we're definitely thinking about it.