Warning: LONG post incoming.
With MKX, NRS took steps in the right direction AND the wrong direction.
Their consistency in the introduction of busted DLC characters baffles me. For MK9, it was Kenshi (and probably Freddy too, but he wasn't used often). For Injustice, it was Batgirl and Martian Manhunter. For MKX, we had Tanya, and now we have Alien. Of course, characters from the initial rosters stood out as well, but the point is that it just flies over my head as to how these characters have flaws that manage to slip past the radar while undergoing testing.
I liked the idea of the variation system, and I would hope to see it return for Injustice 2 because when utilized correctly, it can indeed address the concern of one-sided match-ups...but in MKX, the system's potential was not realized because different variations could play similarly. As an example, Jax had three variations, but all of them leaned towards the same goal: 50/50 offense combined with plus frames. I think a little more variety would really make the system shine.
Other variations were completely irrelevant as they were inferior replicas of stronger variations. For example, as a Scorpion player, can you tell me why I would opt for Inferno over Hellfire?
@PND_Ketchup explains this comparison really well so instead of elaborating, I'll simply link his video. There are other characters who suffer from this, but I'll leave it to you to determine who they are.
For the run meter, I partly like it and I partly don't. What I like about it is how it ties heavily into your use of meter management...in particular, the breakers. This change made us place greater emphasis on the use of enhanced specials, something we didn't see as often in MK9. It also forced you to ask yourself, "Do I want to give up stamina to run in and initiate offense, or save it for a breaker in case I mess up?" However, the run meter returns so quickly that this concept isn't as enforced.
Another con is - okay, you saw this coming - the run cancels. I can't remember when, but I was told that NRS wanted to eliminate the concept of dash cancels from Mortal Kombat 9. They certainly didn't come back in Injustice because of the lack of a block button, which meant that all dashes in that game were commitments, but they somewhat rebounded in MKX because you could instantly cancel runs with attacks or the block button. This, along with advancing normals and strings, made it extremely difficult to play a neutral game.
And yes, when I mention run cancels I also refer to the ridiculous plus frames from A-List Cage and Swarm Queen D'Vorah. They shouldn't be so plus that you have to hold that for so long. At least they decreased the chip damage and meter building from blocking normals to balance this out, but it is still an absurdity.
As far as MKX's 50/50s went, see my post here:
http://www.testyourmight.com/threads/delete-this-please.60179/page-3#post-2101688
The knockdown game - being forced to spend meter to have a chance at waking up is GREAT. Being able to meaty with safe 50/50s is not. I don't even mind if strings last long enough to be used as a meaty or if 50/50s could not be made safe, resources or no.
Backdashes being tied to the use of stamina would be just fine if all characters had backdashes that worked. Some have GREAT backdashes (look at Kano, for fuck's sake) while others are horrible (Kitana and Scorpion, why...?).
The blockstun being bad enough to jack with your punish attempts on certain normals/specials in this game is yet another headache. My character's F2 is guilty of this, as is Kotal Kahn's EX overhead, and there are more examples that could be listed.
While the concept of interactables was tuned better for this game, there are still some that give you invincibility when used
without super meter. That really irks me. I'd hope for them to be gone in Injustice 2, but I'm sure I would be disappointed.
Jump attacks being as they are...yeah. There
is the option to trip-guard them, but I still feel that jump attacks have no business out-prioritizing grounded attacks. If they can't lead to combos, fine, but can I
please smack those bunnies out of the air without the need to use meter?
For those who want me to say it, yes, Scorpion's jump-3 is stupid for the above reason. I'd also like to introduce you to Kung Jin, Jax, Sub-Zero, and Alien.
In relation to jump attacks, there's the concern of an added slowdown to your character's auto-correct before their attack comes out. Your character may have a great D2, but you may have noticed that on occasion, it comes out slower than usual while you're auto-correcting against an opponent jumping over you, and then said D2 loses to their jump attack. I have an eight-frame D2 that sometimes fails to beat cross-ups because of this.
I stuck with MKX for as long as I did because Ninjutsu Scorpion catered so much to how I like to play, AND he was a gemstone from my childhood days when I played the earlier MK titles, but were it not for any of what I listed above I may have put more time into this game than I currently do. I still give a thumbs-up to NRS for supporting the game as much as they did, but they still have work to do...lots of it.