I'm still not quite sure why the consensus seems to be that D-MO is superior to TJ. I totally get that there are major questions about TJ--he's disappeared for two years in the playoffs now, he may be a bit undersized to defend some biggers PFs, and his three-point shot (to be charitable) needs a lot of work. But D-Mo also has a lot of question marks. He's never posted a league-average PER, he was unreliable after the All-Star break last year, he's not a good rebounder, and he's coming back from major back surgery. He was pretty bad in the regular season against key playoff teams such as GS and LA Clippers (look the splits at NBA.com), which does not give and one great confidence that he would have been that much better than TJ in the playoffs. At the end of the day, you have two young PFs brimming with potential, but with a lot of "known unknowns" that will have to be sorted out. The Rox should be patient and see how each develops over the season.
You bring up very good points, but I think the main reason most (or at least myself) feel D-Mo is superior is how he stepped up big when the team needed him to. When we needed him to be the 2nd option behind Harden, he filled in admirably. When the likes of Black, Dorsey, and Papa were getting major minutes in the rotation, he was the one constant that continued to make sure the ship didn't sink. Can you imagine if it would have been Jones with those other 3 in the rotation? We would have likely been slaughtered night in and night out in the paint.
I would venture to say that those splits you are looking at are misconceiving. D-Mo played a good portion of the season out of position at Center, because that is what we needed of him. He is not a Center, and I honestly don't think it will ever be the best spot for him, so it makes sense that he struggled against the Boguts and Jordans of the world. A full season from D-mo playing predominantly at the 4 (across from Howard or another true Center... not Dorsey), and I would be willing to bet his splits against playoff teams would be much better. I honestly think he would destroy Green if GSW tried to put him on D-mo, but unfortunately he was facing Bogut most of the time.
Lastly PER is a terrible stat to compare two players that play completely different such as D-Mo and TJ. Not only do they play differently, but different things are asked of them. D-Mo was asked to bang with the Centers, because we had no other options. He was also asked to create his own offense, because honestly we had nothing behind Harden in that department. Being asked to create your own offense and playing out of position are two sure fire ways to see a lower efficiency or PER. Jones was asked to be a garbage man and slasher. Fight like hell for offensive boards, and cut hard to the rim. That is Jones' duty, and he performs it well. He is efficient because he is feeding off of everything/everyone else. He isn't posting up or working from the elbow. He is solely asked to be a garbage man opposite of Dwight Howard. That's a lot different than being asked to be Dwight's quasi-replacement across from Tarik Black or Joey Dorsey.