I think there's room for 2D and 3D in this world. I've got Aliens: Infestation ready to play and from what I've seen the 2D visuals in that look great. Ultimately, the style of the graphics needs to meet the style of the gameplay, but from what I've been hearing, it works a treat.
In the past, some games have been 2D-ified for handhelds because of processing power and portability. But, like we've seen with SM3DLand, it's possible to have beautiful worlds now in 3D on handhelds. There's definitely a place for both, and there's a certain charm and simplicity in 2D games. The Metroid series is a great advocate for this.
Fused King, you say Muramasa was monotonous, and you're right in one way. However, due to the upgrading aspect and collection of the swords, it didn't seem all that repetitive as it could've been. Those aspects saved the game. Plus, it was just a joy to play and look at. One of my favourite Wii games.
I would be heartbroken if Nintendo phased out 2D completely. They won't, I hope.