(Note: This entry uses a lot of tabletop gamer terminology and assumes the reader knows the meaning of these basic terms).
The biggest change in the M&M 3e rules is the change from D&D-based ability scores to a system more like Green Ronin's other flagship system, True 20. While D&D sets 10 as the average human score in each ability and adds +1 to the die roll modifier for every two points over 10, True20 and M&M 3e/DC Adventures use the ability score itself as the die roll modifier. Thus, the average adult human has a score of 0 in all abilities and every increase in an ability score also increases the modifier. A character can also "sell down" an ability, taking a penalty of up to -5 to die rolls involving that ability in order to gain more points for other abilities (and in M&M/DCA for other character traits).
As much as I love and respect D&D and its place in RPG history (4e aside), I much prefer a system in which your ability score is your modifier. It simplifies things and makes point-based character creation much easier. A bonus with applying this system to a superhero game is that hardly any character will need to sell down an ability, making the system psychologically more palatable.
M&M has always valued all ability scores the same in their point-based character creation system. This has been problematic because, using the traditional six d20 abilities, Strength and Dexterity have always been the most useful abilities in a combat-oriented supers game (with Strength influencing melee damage and a host of other things, while Dexterity affected the accuracy and damage of ranged attacks and the Reflex save).
Green Ronin solved this problem in the new rules by dividing Strength and Dex into two abilities. The new Strength attribute only affects the hero's ability to lift things and perform other impressive feats; the melee attack bonuses now belong to a new ability called Fighting. Similarly, Dexterity now only affects ranged attacks, while the Reflex defense bonus goes to the newly-minted Agility. This change also solves a problem inherent in most d20-based systems: ranged fighters are inherently better than melee fighters because a high Dex improves a character both offensively and defensively.
The new M&M/DCA super power design rules move more in the direction of traditional supers games like Champions, separating flavor and mechanics completely. The Powers chapter mostly lists a series of "effects" that characters can generate, while leaving it to the player to decide what the effect is called or looks like in game.
For example, one effect is called Damage. It allows a character to make a melee attack and force the target to make a Toughness check to avoid gaining an injury. It's up to the player to decide whether this damage happens because the hero's fist turns to stone or because the hero uses special kung fu moves or for some other exotic reason.
This approach to power design can be overwhelming to the novice player, who might not have any idea how effects translate into the kinds of iconic superpowers they see in comic books. Fortunately, the game provides many prefabricated powers as examples of how the process works.
The biggest problem with the book is the way that iconic characters are used inconsistently in examples vs. their stats. For example, Captain Marvel is used as an example of the Activation flaw (which lowers the cost of normally always-on powers in exchange for a requirement that the character take an action to turn the power on). The idea is that, since Billy Batson must say the magic word "Shazam" to turn into Captain Marvel, all of Captain Marvel's powers actually have the Activation flaw. It makes sense and fits with the way Captain Marvel is presented in the comics, but it's not consistent with the way Captain Marvel's stats are presented in the back of the book. There, the requirement to say the magic word is presented as part of Cap's Secret Identity complication and a Power Loss complication that kicks in if Cap ever says the magic word and turns back to Billy Batson.
For the record, I think the way they handled Captain Marvel's powers in the back of the book is the correct way. However, this dual approach also highlights the fact that there's no real guidance about when to use an Alternate Form (heroic) power vs. when to make a transformation to heroic form a mere complication. I think I can figure out a pretty good guideline, but this issue might be really confusing to others.
Despite the minor issues raised in the last section, I still like the system overall. The mechanics are flexible and consistent with the source material (though the power spread of the DC characters may have been compressed a little bit, especially at the upper end). My issues with consistency of presentation are only the difference between an A+ and an A-.