That's it entirely- its not the system, its my unfamiliarity. I have years of experience (dating back to its release in the 1980s) constructing powers in HERO (my #1 system), and while I like M&M (my 2nd favorite system), I've never gotten to actually use it, so my grasp of the mechanics is incomplete. I can design HERO PCs in my head; M&M will take some getting used to.
There's lots of useful stuff at The Atomic Think Tank, the official forums.
My Roll Call thread there has two detailed character creation examples, which should be helpful in learning the character creation system: Minotaur, a powerhouse, and the Martial Artist archetype.
I also have three fights written from the perspective of the players and GM, so they're designed to help people understand the rules (Fights 1 and 2 in particular have a lot of explanation):
Fight #1: X-Men vs. Brotherhood of Evil Mutants
Fight #2: Avengers vs. White Knight
Fight #3: Avengers vs. Overshadow
If you're looking for comic book conversions, the gold standard is Taliesin's Roll Call thread (he has lots of non-comic book conversions as well).