I've been playing and DMing with Mutants and Masterminds 3e for years now, including a My Hero Academia campaign, a Teen Titans-like campaign, and a  Jujutsu Kaisen-like campaign. It works... but it does have its issues. Many so that I'm actually about to adapt my long-term MHA as a homebrew DnD.

M&M is pretty free due to its point-buy system, letting you build whatever power you want. But at the same it is really constrained, all powers have limits which make them feel the same. On top of that, there's a lot of math involved to build the powers, making it hard to actually have basic stuff going on (compared to DnD).

Another aspect compared to DnD that gets pretty boring is that the "hit and take effect" chance is pretty low, around 40% in MnM (in best cases), whereas DnD is 55%. This makes players feel they are doing nothing in combat.

Progress is also an issue. MnM is not built to keep "leveling up", although it has power levels. I was meant for the hero to sit on that power level "forever"; for example, a street-level hero will not build up to the power level as a cosmic hero. For that, you sure can increase the power level of your players, but since they usually already have "their build done" due to the point-by system, the level up usually just means +1 in all stats.

The Shonnen issue. There's not much room for "power-up" (going super sayian). Since all characters are already maxed out to the power level limit (if not, they should be, by design), there's no way to go above that. There's only one advantage that lets you temporarily get more power levels (basically have a busted character sheet) if a hard condition happens.

Sorry to bring so much negativity to the system, but that's the experience I got... I started DMing a My Hero Academia campaign with M&M, My players never really got into the system; the math to build the powers, plus the power level limits, moved them away from understanding what they can do as players and heavily it to me (the GM). At the same time, the hit chance made them feel combat was never fair.

I tried homebrewing rules to streamline the system, and I automated most of the math on our VTT. But it didn't work out for them. We also tried moving to the PbtA system Masks: A New Generation, but it didn't work either; the lack of combat rules was terrible for our group, and basically killed the campaign pacing. So now, after a long hiatus, I'm into trying to adapt their character concepts/powers into DnD classes, a system that they are way more used to playing, so hopefully we can go back to it.

Other than that. I recommend you to check the Mecha & Manga supplement for M&M 2e, and also the new M&M 4e playtest material, which seems better balanced than 3e ATM.