Though the breaker has been a nice addition to Mortal Kombat, playing recently I was remembering an argument one of my friends made when I showed him Deadly Alliance, "As deep as the fighting mechanic's are this game lacks a way to counter your enemy other then the throw button."
Though a parry system was introduced in Armageddon though disappeared right after (except for certain characters that kept it as a special move). But if Mortal Kombat had a counter system similar to DOA, though a bit more conservative, I thought the counter system in that game was good, but the mechanic's relied to heavily on it. Something like it, but harder to pull off.