Wonder if the SNES N3DS XL (itself a year-old release from Japan) is the last of the lot, then.
I've been playing Culdcept Revolt and it's reminded me how amazing 3D can be to even the least action-oriented games. it gives the HUD and UI so much breathing room - your eyes can easily distinguish between different "2D" numbers or icons on-screen, and different monsters or parts of the playing field. The 3D visuals themselves look great with the 3D effect as well, but the way the interface has been built for 3D is superb.
Just to confirm, New Style Boutique 3 does indeed not support 3D either. I just tried the game.
Wow, that's first party and the sequel to a game that had superb 3D. Really disappointing.
Samus Returns seems to be an exception rather than the norm, then, presumably because Nintendo knew that the most enthusiast 3DS owners would be getting that game, and thus they'd own 3DS models rather than 2DSes.