I'm obviously a big fan of M&M. I especially enjoy M&M 3E. That said the system is not without its flaws. The biggest of which also doubles as its greatest strength, the idea of Power Levels.
In theory 2 characters that are PL 10 should be equal to each other. In practice that's not necessarily the case. First, you have the overall PL of 10 which means you have 150 points to spend. You have to check their offensive PLs (Attack Bonus + Damage = 20) and their defensive PLs (Dodge/Parry + Toughness = 20). So you could potentially have 3 different PLs for combat purposes which are only connected to the overall character PL by a sense of what that character SHOULD have. I ran a TT game where we set the PP at PL 8 (120 PP) but allowed for up to PL 10 combat PLs for an X-Men type level game.
If that's not confusing enough you then have to deal with artificial PL inflating (my concept doesn't really call for me to have a Will save this high but for PL purposes I'm going to dump a bunch of points into it...) and powers/abilities that exist outside the PL framework such as teleportation or flight.
I'm sure this is a problem that exists for all point based character generation systems. I'm sure 2 characters made of the same number of points in GURPS or HERO are not necessarily equal across the board. At least M&M gives you defined measuring systems to know where you stand compared to other people of comparable levels. I just think the system could do a better job of letting you know what those levels are. Treat each section as a dial that can be set. How many points can be spent, Offensive PL, Defensive PL, Skill PL, etc.