A few things I've noticed, some probably already mentioned but just in case...
Cyber Sub-Zero's 2,1 is done with the same hand, so shouldn't it be 2,2?
Kano's f+3,3 is done with two different feet. Also, the first hit is done with the back foot, not the front. What a mess!
It seems like Sindel's fireballs don't come out consistently during her levitation. I guess an input bug or something?
Jax's (2,f+2),b+1 is only cancelable into Air Gotcha or Enhanced Air Gotcha. Is this intentional or a bug? Seems like a bug to me.
Sonya's Military Stance 1 is only cancelable into Kiss. Intentional or no?
Reset with Select/Back in training mode does not reset the full state of the game in many cases. For example, Shang Tsung will stay transformed after the reset. Characters will retain armor properties if you reset during the execution of an armored move. For example, vs. Kung Lao, put the dummy to wake up, then reset when he does Enhanced Teleport. After the reset your attacks will be absorbed by an armored Kung Lao.
It would also be nice to be able to reset during an X-Ray, or to hold left/right during a reset to start in either corner.
You cannot manually choose Cyber Sub-Zero's alternate dark blue color by selecting him with Start, because he has no alternate costume.
As far as alternate colors go, while many are great, a lot are still just have minor color tone differences that are way too similar. They should all be distinctly different colors in the interest of making everything clear to the eye, especially in confusing/fast situations. Not only for players, but for spectators/streams as well where everything is harder to see. Some of these even used to exist at some point...where's brown pants Kung Lao? If his damage is getting nerfed, he will definitely need his brown pants. I would also like Banana Sub-Zero.