JG, how much of those numbers are because there is a shortage of ELITE 2 guards in the nba compared to the other positions. Most good guards are PGs now. Also, when teams attack us they have Jones to go after before they go after Harden.
This has been brought up before. Context always matters. Aside from what you've mentioned, PER favors points, assists, and rebounds very heavily. If Harden is guarding a spot up shooter than 2 of those three categories almost completely vanish.
I would argue this was the biggest problem with Harden's defense last season. Over-helping in the lane, essentially to no effect, lead to many open looks for guys who make a living knocking down open looks from 3. The back door cuts were annoying, but the thing that I think altered the outcome of games more is the open threes.
I would counter your statement a bit regarding the state of 2 guards in this league. There is a difference between elite and "star" players. Omer Asik is elite and I think it is safe to say he is no star.
Here's a list of 2 guards that I think are worthy of our respect:
Dwyane Wade
Goran Dragic (he spends most of his time there)
Manu Ginobili
DeMar DeRozan
Monta Ellis
Kevin Martin (Still highly effective except the last 5 minutes)
Aaron Afflalo
Vince Carter
JJ Redick
Gerald Green
Joe Johnson
Lance Stephenson
Jamal Crawford
Bradley Beal
Klay Thompson
OK, let's stop there.....but look at the names I left off....
Kyle Korver
Jimmy Butler
Dion Waiters
Danny Green
Victor Oladipo
Eric Gordon
Randy Foye (turns the ball over too much, but can light it up from deep)
Ray Allen
OJ Mayo
Gerald Henderson
Tony Wroten
Courtney Lee
Those guys are good....and they didn't make the top tier...now look at the list below them...
Wesley Matthews
Marco Belinelli
JR Smith
Anthony Morrow
Gerald Henderson
Tim Hardaway Jr.
Marcus Thornton
James Anderson
Thabo Sefolosha
Evan Fournier
Iman Shumpert
Ben McLemore
We could probably split that group above into two...I don't feel like all those guys are on the same level, but the point stands. There are a lot of quality 2 guards in the NBA. All of those guys in the top group are capable of dominating games one way or the other. I know there aren't many guys like Harden, LBJ, Melo, Durant, etc (That is going to change as more and more teams plug in a PG or combo-guard at the 2), but look at that second group and think to yourself, "man, those guys can all light it up....and they're Group 2!!!! Those Group 1 guys can all flat out school you on any given night!"
The league has it's "stars", but don't let that take away from what, to me, is a solid group of 2 guards. I mean, you are talking about guys who, for the most part, are in the NBA based on one ability: shooting/scoring the ball. So, in one regard it should come as no surprise that Harden's defensive assignments score well. This in no way means I think he is faultless in the matter.
As to your point about teams attacking Jones--there is deeper context to consider here. First, your other point somewhat nullifies this one (if one believes it is true)--that 2 guard is a weak position largely in this league. Pair that with the fact that PF is fairly strong....especially considering LBJ, Melo, KLove, Blake Griffin, Duncan, Pau, Randolph, Davis, Nene, Dirk, LMA, Millsap are out there.....followed by the likes of David Lee, Ryan Anderson, Markieff Morris, Greg Monroe, David West, Taj Gibson, Amir Johnson, Carlos Boozer, and Boris Diaw. All of those dudes can initiate their own offense and are utilized by their teams to do so regardless of opponent. Thus, it skews the thing again. Yes, teams attack from the PF position....but they were going to do that anyways....not just because Jones is out there.
Your point that Harden defends less because of the PF position holds some water. Ultimately, we all know it's the team defense that needs work so his "personal PER" is of little consequence. We know what the deal is far better than PER ever could because we actually see what happens.