So what happens if they fail the check? I am not familiar with Mutants and Masterminds.
As for the discrepancy between classes and HD type, you could add a bonus to the check. Also, if you make it a CON ability check instead of a save, it removes the advantage to classes with CON saves or desire for the Resilient (CON) feat.
Mutants and Masterminds has a damage save system.
Each successful attack requires a "damage save" (think ConSave) vs a DC created by the strength of the atrack.
Failure produces a variety of effects depending on how badly you fail. Degree of success and fail us big.
Succeed - shrug it off
Fail by 1 to 5 - bruised and battered - take cumulative -1 to damage saves until healed. (Think of this as losing hp)
Fail by 6-10 - bruised and get a one turn condition called dazed which is kinda like slowed - limits your actions but doesnt lose all of them
Fail by 11-15 - stunned for one turn
Fail by 16+ - staggered - stunned ongoing - lasting - two staggered equal out
EDIT To give you idea of odds, iirc at beginning of fight if an attack of +10 hits a target with tough +10 its odds are about 25%each of shrug it off, take a bruise, dazed and stunned. So the more severe effects come into play after bruises or when more potent effects hit. END EDIT
These may not be exact but illustrate the idea. Essentially instead of tracking hp up and fow, you use brief conditions as the effect of intermediate combat hits. These produce sudden opportunities and moments of drama- while bruises account for the gradual raising of risk.
Now, the system needs a variety of exploit type options to help add to the drama - like say power attack raising the damage threat of an attack that you can use say against someone stunned. If you had enough of these, conditional, you might even be able to get rid of bruised tracking - or let bruises just extend or exacerbate an existing condition - not just accumulate to penalize saves.
For other genres you could have a wider variety of conditions applied, gradual recovery instead of one round, etc.
All in all, when I used it in supers, scifi and fantasy, I pt produced some of the most dynamic and lively combats of most any rpg system and it scales well and is easily adaptable to produce many different flavors.
This could be added in a lighter touch on top of a hp system, but I have not done so.
I first used it in brief homebrew- I took it in concept from a similar kind of damage tracking used in a tank miniatures game.