The reason he is "rotting", or could "rot" (well, he hasn't been, that's why he has been in the D-Leage), is because:
We have Tyson Chandler as our Center
We have Amare Stoudemire as our PF
And we have Jeffries, Novak, and Jorts who have all produced in meaningful ways, all look legit, have all played huge rolls in our 2nd unit and proven themselves, and contribute unique skill sets to our startin frontcourt.
(elite range/shooting from Novak; range and hustle and toughness from Jorts; veteran leadership, multi-position defender, quality defense in Jeffries).
There is no conspiracy here.
When D'antoni has had decent bigs, they have played, and actually played quite well -- nobody thought Jorts would be nearly as good as he has been, nobody thought Novak would really be crushing like he has, and nobody thought Jeffries would be producing as well as he has either.
Even Tyson Chandler is having pretty much a career year.
The most obvious answer here is the most truthful one: Jordan isnt that good, he has never looked that NBA ready, and we are loaded with high priced, high profil starting fornt court players, and 3 quality, versatile bigs off the bench who have proven their NBA-readiness and game.