I don't think any of them are perfect, of course. It is a combination of different statistical measures (and eye tests) that ultimately probably lead to the best evaluation.
The problem with RPI is that it could be "gamed". As early as the mid-90's we received an article through the WBCA giving the details of how to do it. Authored by an unidentified coach - who wasn't particularly in favor of doing it. I always suspected the anonymous coach was PHS, but no proof.
Of course, they probably all can be gamed, I'm just not up on how to do it.
I don't think LSU's (or other teams with weak schedules) are benefiting particularly under the current rating system, which does reward quads. And SOS factors into NET, as well.