IMO, the entire rating system needs an overhaul. It really means absolutely nothing anymore. The reason we still have the system of G/PG/PG-13/R is for advertising. If you want to get the family crowd, you rate it PG. If you're just concerned about the kids, you make it G. If you want to be a blockbuster and attract the largest demographic of people, you rate it PG-13. It has nothing to do with whether or not the rating is appropriate. (Also, a lot of R movies are split weirdly too; half of them appeal to the horror loving, blood and guts crowd, while the other half are fairly tame except for the controversialness or some language and usually nominated for Oscars :p ).
I feel like we're kind of at a splitting point for PG-13. Like how 80's PG was a bit on the rough side (i.e. "Back to the Future," which has a lot more language than some of today's PG-13's even, but is a fairly harmless storyline). Right now, there's two kinds of PG-13. The first is very tame, with no language or sex and some mild violence (or even suggested violence) and inneundo. They are just barely above the PG level, but are rated PG-13 to attract a bigger crowd. Then there's the other end, where you watch the movie and think "holy cow! why isn't this an R?" (i.e. "Cowboys and Aliens" which, IMO, was far too much on the graphically violent and dark and rough and scary side, along with some nudity).
Trouble is, there's no way to split it. The honest to god difference between R and PG-13 is language. "Frost Nixon" was rated R, but only for one or two scenes where the f-word was used (FYI: the f-word can be used up to 3x in a PG-13 movie before being forced into the R category). Sex and violence really have nothing to do with it. The difference between PG and PG-13 boils down to intensity. TDKR was rated PG-13 for violence and intensity- although the violence was not explicit, it was still happening and I can see how it wouldn't be appropriate for a kid. But I think it's something that a ten year old could handle. But they couldn't give it a PG rating because it would attract kids and parents, who would be offended if they saw it and thought "I can't believe someone thought this was a kid's movie!" Same goes for Avengers-- much less dark and intense, but they still couldn't sell it as a kid's film, even though it is owned by Disney.
It's really all marketing. That's just the way it plays out. But I totally agree with you on whether or not the ratings are right. (I am perfectly comfortable with the new Supes being PG-13, and would be surprised if they posted it as anything less-- or more.)
/end rant./
