MK9 -- Lovable cast of characters. Had a lot of the series favorites. Gameplay emphasized spacing, fine-grained movement with dash cancels, footsies, and pressure. You saw a lot of diff. character archetypes; Kitana played totally different from Cyrax, who was completely diff. from Lao, who was diff. from Smoke, who was diff from Jax, who was nothing like Kenshi, who was distinct from Johnny Cage etc.
Had major balance problems, lots of game engine and design issues, some serious bugs. Those 3 things kept the game from being all it could be.
Injustice -- Pushed the characater diversity even farther by branching out towards anime and hand-drawn-fighter-style archetypes. Crazy traits, flying characters, huge brawlers (Bane is really a brawler, not a grappler), etc. This left some people feeling like they didn't relate to the characters, but for those who liked the comic-book style it was a ton of fun. Despite the footsies being different from MK9, they were nevertheless very important, which is why players like Theo/Cowboy/Bit did well with characters like AM/Sinestro/CW.
The walk speed was controversial, and some very dominant characters spoiled the party in the end. People complained a lot about ending up in guessing-only situations. All kinds of wakeup reversal glitches, corner glitches, etc. added to this. Improved on MK9 in several ways, but the movement kept a lot of people from wanting to continue to play the game.
MKX -- Probably the best core engine of the three. Feels responsive, characters seem to have weight, good depth of interesting character tools, the movement feels smooth. Free of a lot of the glitches that plagued the last two games. Frame data finally puts universal emphasis on pokes and choosing proper attacks, rather than throwing out tons of strings that are + or 0 on block.
The game design pushes almost every top character (with maybe 1-2) exceptions toward one play style. The run button, fast 50/50s, easy long-distance footsie strings, lack of invincible wakeups, massive corner carry, and expensive push block leads 90% of matches to be constant face-to-face mixup-based gameplay. This deemphasizes the great movement, because you spend so much of the match face-to-face rather than moving around in footsie range (with the exception of playing against some characters like Johnny Cage).
---
MKX has the best engine, but it's hard to say in terms of the overall layout and enjoyment of the game which is best. All 3 games are different in their own ways.