Re: M&M 2nd + 3rd (fusion?)
Neither is 'right' or 'wrong', per se. However, I personally feel that 2nd is a better system. The primary changes from 2nd to 3rd were adding in two new defenses you had to buy, while stripping out drawbacks entirely (making them complications). All while keeping point totals the same. This means that things got a LOT more expensive, essentially forcing people into 'archetype' characters. Someone like Cyclops is still easy to do, but someone like Iceman is more difficult than it used to be. In 2nd, Drawbacks were, essentially, the opposite number of Feats, just as Extras are opposite Flaws. Reducing costs or giving more points encourages players to put weaknesses in their characters. To me, a character like Superman is utterly boring, while Batman or Rorschach are incredibly compelling. It is the flaws and weaknesses that make superheroes compelling for me, not their powers. This is also one of the reasons I like Hero System better than other systems, as the game design takes this into consideration, so that you don't get the full measure of points available unless you take disadvantages. And every disadvantage is a potential plot hook the GM can use to draw you into the setting and character.
To make a parallel, it is akin to the difference between using pregen characters in convention play, and using the character you made yourself in your weekly game that's been going on for a year now. Both have great potential for fun, and I wouldn't slight either one out of hand, but the second one offers the chance for a richer and more fulfilling experience. Or, if you prefer, compare getting a bucket of fried chicken from KFC to grilling up steaks on the grill outside. Both are good, in their way, but still...