Sounds more like rejecting the premise than rejecting the system to me. The story always comes first, and the mechanics are only there to support that and add a little randomness and fun. If, in terms of narrative, you want Batman to be able to dodge/block/whatever Superman's punch, you come up with a rationalization of that. In the comics it might be a "wtf, how did he do that??!" moment, followed by a flashback where you see Batman preparing for that eventuality, and using some BatPlotDevice gear that uses kryptonite to weaken and slow down the punch at the last millisecond, enough for him to dodge, or maybe Batman turns out to have been a hologram for the whole scene, or whatever.i agree that it can be, but if we’re talking about a mechanic whereby a hyper-skilled but otherwise mundane character- IOW, a Batman, not a Longshot- can thwart a “trillion mph” punch, that’s a system I personally wouldn’t want to be playing.
Now, assuming you wouldn't reject the rationalization presented in the comics (which is possible... I mean, comics often have very dumb and implausible plot twists, so it's ok to say "this is bullshit, I don't want to read this"), then the key is to figure out how to represent that in terms of mechanics. If you're OK with "flashback mechanics" like the Preparedness rolls in Gumshoe, you can have Batman roll for that, retroactively declare that yeah they have the BatPlotDevice, spend some extra points, and that takes whatever numbers aways from Superman's roll, maybe enough to indeed survive the attack. In something like HeroQuest or FATE or SavageWorlds you might spend some HP/FP/bennies to do that, but you would also have to work with the GM to justify what's going on (i.e: BatPlotDevice, hologram, or something else)... it's not like a free ride where you get to change the story without explaining how in the context of that story. Just saying "I spend the points and I dodge it" is not OK.
There are plenty ways to go about it depending on the system. My point is that the mechanics are irrelevant at first though -- the question is whether that story is OK or not. If it is, the GM will figure out the rules to make it happen.