Oh, I can think of a few things...
a) Unblockable interactables, with hindsight, were a very poor choice. Thank god they're fixing it for MKX, that's all I can say.
b) The messed up block damage system. MK's block system works well because it's clearly focused on offense rather than defense, so most any move can do decent block damage. SF's block system works well too - having block damage only on special moves, and set at a regular 25% of normal damage, keeps the game defensive, but still encourages defense beyond simply blocking all the time.
Injustice attempts a middle ground between these two and falls flat on its face, especially on multi-hitting special moves. Making it so that every hit on block does at least 1% damage was very silly (there are only a small handful of exceptions to this 'at least 1%' rule IIRC). Coupled with the extremely limited block damage on normals, it ultimately leaves characters with safe, multi-hitting special moves at an enormous advantage on that front. The best example of this, naturally, is Aquaman's Trident Rush. Injustice should either have buffed normal block damage, or normalized special block damage, because the system as is just doesn't flow smoothly.
c) While MB b3/f3 was a great idea, and on the whole works well, a lot of the time characters end up being very reliant on this tool. Either MB b3 provides an answer to way too many tools at once, or it's pretty much the only answer to certain other tools - that needs to be balanced somehow. That said, bounce cancels requiring two bars of meter rather than one is also ridiculous - for most characters there's simply no justification for using that much meter, even if it would provide a strong combo.
d) Unless it's an MB move, there shouldn't be more than one projectile on screen at any one time. If that's too harsh, there definitely shouldn't be more than two.
e) Raven's walk speed should be set as the 'average' walk speed which everyone else is based around. Or make the stages smaller on average. But only one of those two - the walk speed wouldn't be as big an issue if the stages weren't so damn big lol.
f) The ridiculousness of 'levitating' characters having certain moves whiffing on them when they should have hit. This used to be a big problem with Harley and b22...
g) The 'MB version only comes out if initial part of special move hits' aspect of many specials. IDK, I personally preferred the MK system where you have to commit to the one bar of meter before using the MB...
