I can't speak for anyone else, but this is my view on it. It's pretty long so I have a TL;DR at the bottom.
It would have to be due to MK9's character design. NRS appeared to have designed it so that no two characters would play exactly like one another, each character being unique was important. As such each character could develop into their own as the game went on (becoming a rushdown, zoning, footsie, etc. type character by the end).
In this, developing a fighting system would be more straightforward in that each character would exist as a microcosm of a basic 2D fighting game.
Basically, every character would have an anti-air, footsie tools, etc., etc. And depending on the design goals they would tweak the character's playstyle through their identity, although depending on the character, it's your opinion on whether or not the design was successful.
A conversation like this most likely happened during development for example: "Smoke could be a keep away character, but not too strong in that he would be able to stay away all game", so he'd be a more mid-range footsie based character with a reactive playstyle. Some players thought it was fun, others thought it was frustrating, but all in all, Smoke had his own identity.
All in all MK9 was successful in establishing a unique identity for each character, the problem arose from balance and bugs. MK9 was a basic 2D fighter with unique character identity.
__________________________________
MKX doesn't feel to have this.
MKX is created, now they seek to do this with each variation and on top of that they introduce the run system, interactables, stamina, etc. So instead of the "basic 2D fighter" from before, they go the route of "if everyone basically has a 50/50, then it's balanced" type of 2D fighter. I'm not saying this is what they intended to do, but this is what the finished product feels like.
Additionally, there's a sinking feeling I would describe as the characters exist as pieces, not their own entity.
Say a character like Rain was playable in MKX, they want to make it so that there's a "rushdown Rain", "zoning Rain" and "footsies Rain".
Well, if you're a die-hard Rain fan you're gonna try playing all of them. But unlike MK9 where your character simply has all the tools out the gate, every character in MKX feels like they have something "taken away" from them.
So you might like the "Zoning Rain" variation, but not "Footsies" or "Rushdown" Rain.
So you have to go find another character that does fit your playstyle, but you're a Rain fan so you try to play someone else and get bored with them.
TL;DR: MK9 was basic fighter, and every character feels unique, but game is very unbalanced and buggy. MKX was basic fighter with a lot of crap so ends up making "50/50" game and variations feel like fragments, not a whole character, game is also unbalanced, but not as bad as MK9, but ends up unsatisfying anyways.
