I can't speak for Green Ronin, but I know that Natural 20 Press's Four-Color to Fantasy, which is out right now, uses the level system because it is meant to be used with existing systems. I admire GR for how they fiddled with hit points; it's very nifty. However, using what I've heard of M&M, I'd have to say that it misses out on being system-compatible.
Sure, a superhero game is nice, but if you're already writing the rules for superpowers, why not open them up so you can use them for things other than just the one game?
This is what FCTF does. We have all the rules you'll need to play a superhero game, though we assume that you have some other D20 core book to base the rules on (e.g., you want a modern superhero game, so you take d20 modern and add the super powers; or you want a super-spy game, so you take Spycraft and add super powers). Since we use the level-based system, these rules are compatible with most other d20 systems, letting you balance encounters, assign experience, and make sure that the game is challenging without being deadly.
However, since the rules are totally compatible with the core D20 system, you can use them for things other than 'super powers,' in the comic book sense. If you're playing D&D, you can use the superpower rules in FCTF to give magical powers to villains, or to create balanced Level Adjustments for powerful races. If you're in Spycraft, your spy might gain some sort of super-gadget that gives him a permanent enhancement, and our rules will let you know how powerful the ability is. In d20 Cthulhu, maybe your character gains some sort of freaky otherworldly power from his exposure to the Old Ones. You can use the super-power rules to handle those.
So while M&M seems to be fully fleshed out as its own superheroic genre game, Four-Color to Fantasy is flexible enough to handle that and then some. I could get into a long discussion about how levels provide a clearer goal for players, thus encouraging them to keep interested in their characters. Incremental advancement might be more realistic, but it's not as fun to play. I'm also willing to go into depth about how with FCTF you can handle advancement of practically anything the character wants, from skills to combat ability to super powers.
If you're interested, I can talk more about it. I love to show off how flexible and nifty it is.
p.s. One caveat, though. It's our philosophy that in a roleplaying game, how you play your character is a matter of personality, and that emotional drawbacks don't balance physical powers. Thus, you won't see things like "Hates Orcs" in FCTF. If you want to hate orcs, then your character hates orcs. Your super powers and skills determine how powerful you are; your personality is there for the sake of roleplaying.
p.p.s. Another caveat. If a character has the powers of a god, then don't try to stat him. Other non-god characters probably can't him in a toe-to-toe fight, so his specific power level is unimportant. For the same reason that I can rule that a supernova will destroy the planet (even though there's no exact listing of the damage a supernova deals), you can rule arbitrarily what a god-level entity can do. If the PCs are also god-level, then I'll be the first to admit that our rules in FCTF cannot cover them.