Alright, I have a little bit of time on my hands so I'll write out exactly what I have to say. I don't think I've written anything like this on this board, but my feelings are pretty well known.
For those who say that PER works because the top few players are always the top few players in the NBA at the time, that's basically a load of crap. For starters/guys who play 50 minutes a game, you can come up with almost identical results by doing the most rudimentary statistical math. A simple formula like points + rebounds + (assists x 1.5) will spit out almost identical results to PER with exceptions (point guards having big assist numbers usually being the exception). So really PER isn't some revolutionary concept at all, it's basically "best stats wins".
The main problem with PER comes when you try to evaluate a player's worth on it or when you use it compare primary ball handlers with third options or struggling starters with energy guys off the bench. PER *CLAIMS* to be capable of doing things like this, but clearly it fails. Things like Carl Landry as a top 10 player IN THE LEAGUE or Manu Ginobili being top SG (over Kobe during his MVP season) show the failure of PER.
What humans know that machines don't is that a player's worth can't be based on statistics. A guy like Bowen could be useful to a team even if he shoots only a couple times a game, gets a handful of rebounds and a couple steals. His production can't be measured by stats. But even going beyond that:
Assists don't measure passing skill. Generally the person with the highest assists are the best passers, true. But an assist is contingent on another player making a shot. The assist stat doesn't differentiate between a brilliant pass that creates a wide open shot/dunk and a pass you make with the shot clock at 2, where the guy jacks up an awful shot to beat the clock that just happens to go in. Statistical reward is identical in both cases/PER reward is identical. Clearly the eye can differentiate here where statistics cannot. Also, all assists are not created equally. Last year during the Chris Paul for MVP campaign, the author of this blog:
http://20secondtimeout.blogspot.com/ tracked Chris Paul's assists. He found that Paul was being credited with assists in areas that almost every other player in the league was not being given an assist. Official scoring was actually being influenced by reputation! It's like saying "who shot that last shot? Kobe? Well...even though it didn't go in, I'll give him 2 points anyways" or "who got that last board? Wally Z? Well...Lebron was in the area, I'll give Lebron credit instead". Utter ridiculousness and yet something like this was a fundamental of the stat. You cannot create an accurate statistic if fudging like tihs is acceptable.
Then we get to usage and role. Usage is theoretically a part of the PER statistic, however it is not. The players with the highest usage generally tend to have the highest PER. 7 of the top 10 in usage right now are in the top 11 in PER. And 1 of the other (Carmelo) will be at the end of the year. The moral of the story here? The more you have the ball, the more statistics you will accumulate. And that's the moral of PER.
PER claims to be something that accurately measures a player's statistical contribution relative to their role and play time. And this is why it is a failure because it does not do this. The player who handles the ball more, accumulates the most points, assists and rebounds moves to the front of the line.
If you accept the premise that the man who accumulates the most points, assists and rebounds is the best player in the league then fine. But if you think that there's more to the game of basketball and to a player's worth than raw statistical accumulation then you recognize the problem of PER and the problem of assigning worth to a player by stats.