I'm not disputing that the rating system is flawed--perhaps even badly so. But with the examples you gave (and others in the thread), I just keep asking "so what?"
From a business perspective, the MPAA is one of the most effective tools the big studios have to lock out competition.
When Trey Parker and Matt Stone submitted their independent film Orgazmo to the MPAA, the film got an NC-17 for scenes of nudity (which for what it's worth barely amount to anything offensive). They asked the MPAA what to change for an R rating, and the MPAA said they were merely a ratings board, and that giving suggestions would make them a censorship organization. Since Orgazmo was made before digital editing, Parker and Stone decided not to spend the large amount of money necessary to recut the film merely hoping to get an R rating.
Fast forward a couple years to the South Park movie. They submit the film to the MPAA and get an NC-17. Again, they asked what to change, and the MPAA gave them a very specific list of reasons why the film was rated NC-17. Even so, as the movie got within a couple weeks of release time, the rating didn't change. So essentially one of the movie's producers got on the film with the MPAA and "convinced" them to change the rating.
When Orgazmo was an edgy film that could take business away from the studios, the MPAA shut Trey and Matt down. When they were working for the studios, the MPAA eventually caved to them.
Another obvious reason the MPAA sucks is reducing R-rated films to PG-13. This is a getting a little less bad than it was even a year ago. Slowly studios are starting to realize that just having an R-rated gritty film will give you business. But movies have become stupidly sanitized in the name of getting teenagers into the theater. Think about Terminator 2, Total Recall, or Die Hard without the proliferation of our favorite word (fuck) and the blood and guts. If you want to see an even more specific example of why forcing films to be PG-13 sucks, watch the unrated cut of Live Free or Die Hard. I'm not sure how tangibly different it really is, but the extra bloodiness and filthy language make it a noticeably more engaging movie.
And then there's the lack of transparency and qualification in the organization.
I agreed with the film's message but their method of basically stalking board members was kind of fucked up. It was fun to watch but it wasn't a very professionally executed documentary. It felt like a sleazy TMZ piece at times.
This was actually my favorite part of the movie. Anyone on the internet can compare parts of different films to show the MPAA's inconsistent standards (though not necessarily as well as TFISYR). But actually investigating who the board members were to prove they're basically a group of random people and rattle the MPAA's cage a bit was AWESOME. And it gets to the real heart of why the MPAA sucks.
Being a middle-aged man/woman with kids doesn't even necessarily qualify you to raise kids, let alone make potentially multi-million dollar decisions about movie ratings. And the intentionally obfuscated nature of the process means it can't really be challenged. The MPAA is designed to purposefully stunt artistic expression and reduce freedom of commerce, and the studios want it that way. And then I go to PG-13 movies and see violence and sexual content I'd never want my hypothetical 13-year-old kid to see anyway, so it's serving these nefarious (I know that's a terrible and cheesy word, sorry) secondary functions at the expense of its primary function. Everything about the MPAA is wrong.
I hope that helps.