Here is the real reason, because you might be too young to remember.
Being 3D was a fad during the 90s. Everything had to be 3D: RPGs (FF7), Fighting games (MK4), Puzzle games (Tetris 3D) and yes, even plataformers.
It started with PC gaming making 3D card brands a war akin the Sega/Nintendo war years before, which games that simply didn't work unless you had the latest models of NVIDIA, 3DFX or AMD video card. That fad began dripping into consoles when the SNES released faux 3D games (like Donkey Kong Country) and rudimentary 3D games (like Star Fox), but by the end of that generation is was full blown. So hard it hit, that the next generation of consoles were build with some extreme 3D integration, so extreme that many consoles (like the N64 and PS1) barely played 2D games. Believe it or not, MK 3 was harder to make and run efficiently in the N64 hardware than something like War Gods. This, together with the publishers mandate that saw this self fulfilling prophecy and interpreted it as "no one wants 2D, everything has to be 3D", made 3D the new bare minimum. Every single game (with some notable exceptions, like Guilty Gear) had to be 3D, even when they didn't have the budget or the horsepower to make more than a couple cubes and pretend it was a face.
That forced the transition of some franchises into 3D and the result, for the most part, weren't pretty. Look at Street Fighter EX, Castlevania 64 or Earthworm Jim 3D for some examples... It took almost 15 years and the entire indie community for people to realize that 2D graphics games aged a lot better than early 3D graphics games. Sure, there are some good games in that era: Mario 64 and Metal Gear Solid are still considered masterpieces, but 90% of the other games were extremely flawed. It was natural, most of them were forced into a perspective they didn't understood, weren't designed to support and had a lot of problems they had to solve on the way. They were exploratory in a way most genres weren't since the Atari days, and hadn't need to be until the introduction of VR over 20 years later.