There is one basic reason for the screwy things that happen with MPAA
ratings: ratings are marketing
The 'R' rating is a very, very cheap advertisement aimed at people under 17. As a teenager, you know that an 'R' rated movie is gonna have what you want; sex, violence, swearing, etc. Plus, you're "not supposed to" see movies with an 'R' rating if you're under 17 (not that this has any basis in law anywhere...the ratings system is not law, or anything like a law). As we all know, a basic fact of adolescent existence is the desire to do anything and everything you're "not allowed" to do.
People were tremendously upset when it was revealed that studios had been testing trailers for 'R' rated movies on young kids. I, for one, couldn't understand the surprise. Because that's exactly who they're marketing to. This is not a secret.
Directors are contractually obligated to deliver a film with a certain rating. A studio makes an initial decision in pre-production (which can, of course, be revised during production and post-production) as to who the audience for a given film is. That is, who they are going to market the film to. This decision is, obviously, based on how they think they can make the most profit from a given film.
Any movie that is seen as having primarily a teen audience is steered toward an 'R' rating. A film that may be thought to play well with families is sent in a 'PG-13' (which is a rating that was specifically invented for "Indiana Jones and the Temple of Doom") direction. You'll note that there are, essentially, no more movies rated simply 'PG'. In a very quick, informal study on the IMDb I could not find a major Hollywood film with a 'PG' rating after 1989.
And then there's the 'G' rating, which Disney and Don Bluth seem to have a virtual monopoly on. 'G', like 'R', is a gigantic profit source, especially on video.
Studios do not just make films and then submit them to the MPAA and take whatever rating may fall upon them. Films are, from the very beginning, designed to wring the most marketing possible out of the ratings system.
There is a whole separate discussion about the standards of the MPAA...why is violence accepted and sexuality censured? Why is homosexual sexuality rated "more strongly" than heterosexual sexuality of equivalent explicitness? Why is female sexuality (active sexuality, not passive, objectified, traditional sexuality) looked at with a harsher eye than male?
And why do we allow a private group of "concerned parents" inflict their personal morality on the rest of us?
And, most importantly, why do we provide one more mechanism by which parents can use an external, superficial source to decide what's "right" for their children rather than taking an active role and doing their own research?