Mutants and Masterminds: I don't see how its complicated (everything's just based off of 1d20 rolls), but it certainly can feature power balance issues. In my tabletop campaign with the 1st Edition rules, for example, I had a player who could Boost and Heal herself and other PCs to a degree which was ridiculous and totally unbalancing. The 3rd Edition rules (which is what the new DC Adventures game uses) looks more solid and accounts for more power level considerations - but its still a game that relies on GM oversight and an understanding at the table of what is and isn't fair. The rules admit as much.
Wild Talents: Wild Talents is theoretically faster via ORE (One Roll Engine: everything's based off finding matches in a pool of 1 to 10 dice), but in practice I've found it to be about the same speed as M&M when you account for people trying to figure out when things happen relative to one another and the effects of their actions. You can shave off some complexity like Ross did in the Age of Masks game, however, fudging the details to keep it quick. Balance wise, I'd say its got less loopholes than M&M, but it also has sidebars where they mention how it can get totally out of whack if your players like to Optimize without some GM feedback. In a WT PBP game I'm currently running, I've discussed letting people redo some stats since the guys with big die pools get the shaft relative to those who (more wisely) invested in Hard and Wild Dice. I'd run Godlike before but I forgot how much of a vast gulf lies between them.
Y'know, I can't think of a single superhero system worth a damn that doesn't have potential for absurd and unbalanced character builds. If you have player crafted abilities and offer ways for them to tweak the costs and potency, initial balance gets a lot fuzzier. What at first seemed "weak" can become monstrous in actual play, and what first seemed "overpowered" can be watered down to becoming essentially meaningless. You can TRY and lock down abuse by systems on top of systems with layers of cost controls (Hero is probably an example of this), but those pesky players will still find a way.
Ultimately, its probably best to get on the same page with your players about what the power level of the game is, review all stats, and be open to fudgery and tinkering if/when things don't line up like you all feel they should. The system can spin this, but I might argue it has more to do with how much crunch and workload you all like more than anything else.
