The biggest reason this isn't the case I believe is because they're waaaay to similar in nature.
Dead on. Which is why I keep pushing for and hoping that the gap will be further set apart with each installment. The more different the two series are, the more likely that people will play both titles as opposed to dropping one for the next one.
Leave all the rampant unreactable OH/Low starting 50/50's, free +frame on block run cancels galore, godlike near impossible to AA Jip's that lead to free pressure/mixups/+F, Armor everywhere, half screen advancing fast safe mids, running, small stages, 2 bar full stamina m push block, and variable block stun in the MK series and keep it there for people who like that gameplay.
For Injustice, simply improve on what worked the last game, improve the things that didn't work well like needing a faster walk speed/the damage and blocking interactables/etc, and moving its gameplay style as far from MKX as possible to even more of the good elements of Inj.
With the return of characters keeping their moves from Inj1 to Inj2, and rumors that it is much more footsie based than ever, I can only hope that this is the plan.