A criticism, some ranting, and a compliment or two...
I don't think there's anything seriously wrong with the ruleset, but I think that showing the breakdown of power construction would help a lot when determining how powers interact, react, etc. For instance, Alternate Form: Energy includes Ghost Touch on the Energy Blast. This is necessary for the power to affect things in the real world. What it also means is that anyone in AF: Energy form will affect other Incorporeal characters as well. Now, I know this because it's been discussed online and Kenson has said that AF: Energy indeed includes Ghost Touch. The interaction part is my conclusion, but that's my job, I'm the GM. Most of the powers listed are easy to break down and deduce interaction, but an explicit listing for each of the sample power builds would help immensely.
A word about "front-loaded" powers and game balance: cost isn't the only balancing factor. I have yet to have a real problem with Invisibility or Incorporeality. First off, it's completely in genre to have villians with abilities that either diametrically oppose the heroes, or specifically target weaknessess/overcome abilities. Second, I think that traditional gameplay has inflated the value of powers like Invisibility, and the always tricky "At what point do you not make things touching you invisible?" The arguement goes, "If I make my clothes invisible, why not the flour that guy just dumped on me?" The simple answer is, "Well, all the flour touching you is, yes, invisible too, but that just means you make a man-shaped hole in the cloud of flour dust now in the room."
The same is true for rain, dust kicked up by a well-placed Energy Blast ("I use a hero point to gain See Invisibility as a power stunt of my EB"), or a fight in an active sawmill. Whether by environment or a well used power, small particulate matter is a traditional and in genre counter for invisibility. Also, Invisible characters leave tracks and make noise.
Mechanically, Invisibility is countered by a 2 different superfeats, Blindsight and See Invisibility. Also, low level Invisibility is useless for a melee character, as anyone within 5 feet gets a Spot check v. DC 10+(Ranks in Invisibility) to notice him. A ranged character can benefit from 1 rank, true, but after the first shot, everybody knows where she is, and once they get within 5 feet, she's toast. To get around it, she'll have to buy the Subtle extra for her attack power, effectively negating the cheap cost. Even so, how does Telescopic Senses factor in to the "within 5' " determination? If Telescoping Senses eliminates range penalties, effectively giving you unmodified Spot checks at distance, then wouldn't a character with Telescopic Vision get that Spot check v. Invisibility at a distance?
Does this mean in my games I nerf Invisibility? No. Invisible characters generally get the drop on their opponents, can recon relatively safely, and still get the benefit of concealment even when Spotted. But with all the ways to be detected, I don't think that's worth more than 1pp/rank. Also, it's advisable to let your players know in advance that in a supers game, being Invisible isn't as effective as it is against orcs and goblins.
Incorporeality is a problem, but only if you let characters be generically intangible, which is against the intent of the system. A supers character has a defining concept, one that determines a lot about his interaction with the game world. Made of light? OK then, we automatically know that you're affected by darkness and can't pass through opaque objects. Made of fire? Then water's your bane. Constantly vibrating so that your molecules "sift" through solid objects? You're going to have a problem passing through materials with a base hardness higher than your ranks. Are you a ghost? Then mystical powers and substances will give you cause for concern.
One thing that I love about the MnM book as written is the constant emphasis on GM interaction throughout the book. GM's ignore this at their own peril.
While benchmarks or point caps would make it easier, I like the fact that they were omitted. This allows each GM and group to determine their own level of play. For instance, at what PL would you set a Batman style game? In MnM, it doesn't matter that nearly everyone has a different answer, because you can do it at whatever PL makes sense to you and your game group.
I like MnM mostly because it just gives me the tools I need and then gets out of my way.
J