I have a problem with there being a separate bar for super like people suggest. MK9 was hype because the life lead meant A LOT. MK9 was the anti comeback game in a day when Marvel was the hot topic and it was fashionable to integrate easy mode comeback factors.
If another bar is put in for super that only fills from taking damage it means you are giving your opponent the tools to beat you by winning. How dare you take your opponents life! I think the meter one gets from taking damage should be low in fighting games. Sure that makes it hard to to come back, but that is what makes it exciting to watch.
I think they should keep breaker the same and just have a "cool down" for it where you can't break for a set amount of time after you break the first time. Something like that would be good.
Also for supers what they need to do with them, instead of giving them a separate bar, is have them give a certain amount of guaranteed damage in combos. Something like 10-15% or so. That way it would make more sense to use the X-ray. In MK9 they scaled horribly and unless you were going for unbreakable damage there was little reason to use one. With better scaling the choice would between blowing all your resources on one giant combo that does 60+% or saving it for something else. That can be your comeback factor...the original comeback factor.