So, as it seems, waging is back, or something that looks like it! Batman and Atrocitus clashed twice in the footage shown, where they stood up close to one another with just one of them gaining the upper hand. We don't know how it works though, as the HUD was hidden, so whether it has been changed or stays the same from the first Injustice remains to be seen.
And another note, Supergirl has Fujin's whirlwind throw where she spins around herself on the spot, creating a small tornado and then sends it towards the opponent.
Also, Ed Boon talks about the reason characters look different with different armour and such, is because of "personalization"! What that specifically means, we don't know, but it does sound like somewhat like I had described in my theory in another thread, where you can customize your character with certain armour pieces which will change the way the character plays.