While I agree that the MPAA ratings are flawed, I don't really think there could be a "perfect" system. Different things are always going to offend different people, and you can't ever completely regulate that.
As others have said, things have changed somewhat over the last 30 years or so, but it's a strange dichotomy. Sure there are some PG-13 films that probably would have been R not too long ago, but there were several PGs in the '70s that would be R nowadays.
That said, however, I think the main problem is not so much the system itself, but rather people's perception of it (not all people, obviously, but many).
What I think has happened is that the proverbial "edge" has been pushed further and further, and now no one is really sure where it is. In the late-'60s and through most of the '70s, most kid- and family-oriented films used to be rated G, and there were more than a few adult-oriented ones that got a PG. But "G" attained a stigma of "kiddie-flick," so they started adding some slightly edgy content to make certain films PG so more people would go to see them. Gradually, throughout the '80s, "PG" came to be thought of as "probably okay for kids." Thus the PG-13 was created in 1984, because parents thought that Indiana Jones and Gremlins were too violent for PG (and by that point, they probably were). Now, when they want more "edge" than a "kiddie-flick" they have to go for PG-13, although even that is becoming less-and-less so.
Anyway, that's all just speculation; just an opinion based on what I've observed. When all is said and done, I just wish that parents would be parents and understand that the ratings system is not, and was never intended to be, the end-all, be-all of what is appropriate for their kids. It was merely intended to be a warning of possible inappropriate content. It is still up to the parent to decide what is right for their kids; the ratings are just meant to help a bit.
I do agree, though, that they have been incosistent. I would have given the uncut Requiem For a Dream an R, Whale Rider a PG, and the director's cut of Amadeus a PG-13. And it's true that many PG-13s are either pumped-up PGs (Spider-Man 2 probably could have been PG, except for the Evil Dead scene) or toned-down Rs (Minority Report did push it).
I don't really know what could be done, though. Like I said, I don't think any system would be completely perfect. I do think the current system itself is okay, but people need to try to understand it a little more. Just my opinion, though.