@Runescryer
I headwizzed an OC comic book MU running M&M 3e for a little over three years (Project Prometheus). By the end of our run, some of us were still quite happy with 3e, while others absolutely wished to chuck the whole fucking thing into the ocean. 3e honestly feels like it's meant for a particular TYPE of comic book style of play. It's all explosions and zero tension, unlike the far more interesting (IMO) 2e, which at least gives a GM room to challenge his players. Unlike 3e, the PCs can lose in 2e.
Your chief problem tends to be the Hero Point/Villain Point system, which creates an asymmetric environment where one side gets a large number of 'do-overs' and general invitation to step outside of the rules as needed. If it's done correctly, heroes will generate HPs throughout the combat because they should be nailing their complications. They spend them as desired and get to do all sorts of heroic things. Villain Points are supposed to be the GM's response to HPs, but they just don't work very well because spending a VP against a PC gives that character a HP as a consolation.
It sounds good on paper. In practice, it's obnoxious and terrible for any sense of tension.
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Hero attacks villain and misses. Hero spends a HP for a reroll with advantage. Almost certainly hits.
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Hero attacks villain and misses. Hero spends a HP for a reroll with advantage. Almost certainly hits. GM spends a VP to mitigate the damage, and awards the hero an HP. Hero... spends an HP and attacks again.
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Villain attacks hero and misses. GM spends a VP for a reroll with advantage, immediately awarding player with an HP. Villain hits, hero immediately spends an HP to mitigate the damage (gosh. Who could've seen that coming?)
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GM decides he wants to create an area attack where there wasn't one before. GM is an idiot. This one action means every PC in the blast earns a HP. For fuck's sake. No. Stop it.
It rapidly becomes apparent that either the GM has to accept that villain points are just for show, or the GM has to be very, very careful about when he or she spends a point.
It's even stacked from the beginning. In any given game, there are a lot more HPs on the table than VPs. I forget the formula, but most PCs will have 2-3 HP and the GM will probably have something like 4-5 VP. In a 4 PC game, that's 12 HP and 5 VP at the start. This wouldn't be so bad (the heroes should usually win, so what's the harm of helping them out?) if it weren't for the reflexive nature of spending a VP and that the heroes are going to get more. It can easily get out of hand.
At the very least, you really should regress to the 2e HP system. I haven't even touched on the fact that due to this absurdly asymmetrical reroll mechanic, all the luck powers ONLY WORK PROPERLY with heroes (and are utterly broken as fuck).
Then you'll find all sorts of other weird and wonderful idio(syncra)cies in the combat feats. I forget the names of the combat feat and can't be assed to look for a book or pdf, but there's some feat that allows you to make an additional attack if you drop a minion. This has been with M&M since the beginning. The difference is that in 2e, it had a melee requirement. In 3e, they don't care how you do it. Melee, ranged, area, it's all the same.
In practice, this means the last place on earth any villain ever wants to stand is ANYWHERE NEAR HIS MINIONS. Seriously. Stay the fuck away from me, man. You drop an area burst right on that villain and hit like 10 minions, too. Villain makes a damage save along with 10 minions. Let's say he loses 3 minions. OK... so, that feat says you get to do it again! Now the villain and his 7 minions make another round of damage saves. Drop 3 more minions, right? You see where this is going. Not only is this stupid as hell, but the entire thing is completely asymmetrical.
In 3 years of GMing 3rd ed, I don't believe I ever had a team of PCs lose a combat. It never even came close. The only way I could challenge players was by facing them with unfair PL/PP totals, and that's just bullshit. We errata'd a bunch of things, but I feel we should've gone way the fuck overboard.
3e looks good, but it's not really much better than traits. That said, it's actually a great system if you want to go with some sort of edgy 'if you lose, you are dead' setup. It looks scary to the players, but they can't possibly lose. 2e is a gem and I highly recommend you look it over. I'd use that over 3e. Just my two cents.