It's because pixel artists have to draw every frame of animation and it's not as easy to change the models or animations on the fly (flexibility helps with larger production teams). While it risks losing money for large companies, indie devs don't have a publisher to answer to. However, that also means they likely don't have the means to find and hire someone who knows how to model and animate 3D objects, while almost anyone can make 2D art and animation.
when the switch from 2d to 3d only happened, it was still much harder to do 3d. i’d argue it still is, in most cases. when the startup cost to make pretty 3d is so high, it sure seems like it’s much cheaper to just hire artists to redraw pixel animation. especially if, as you say, anybody can do it.
while everything you said is totally true, it seems like you’re painting a picture of 2d and pixel being too risky for big companies. i honestly don’t agree with that, nor do i think that’s the reason they don’t do 2d more often. i think the problem lies more in investor pressure, and an assumption that the vast majority of buyers are only interested in “new tech”.
while i sorta get companies like EA being afraid to do 2d, i’m surprised that such a nostalgia-driven, retro-oriented company like nintendo won’t give it a shot. they already include so much 2d fanservice in games already, so why not go all the way? but i’m probably expecting too much from n. shig seems to be very afraid to let anyone experiment with any of his old ip, nor is he willing to let any major changes be made, meaning evolution and growth is unlikely. it also means we won’t see him allow smaller indie-style teams make a cool, experimental new 2d mario game.