"the Marines run an aircraft acquisition program is akin to letting USAF run an amphibious ship acquisition program. It simply isn't their specialty"
Perhaps I didn't take the post in the tone intended. That said, you might want to check who does the procurement of amphibious ships. While the Marines have input, that bus is driven by the Navy. Spend some time on a LHD sized ship and you'll find plenty of unwanted compromises.
To the above, no it's not their specialty, but it's an aircraft that is largely intended for the Marines use. Dove tailing nicely to that, The bulk of VTOL experience within the military resides with the Marines.
The tail shouldn't wag the dog, I would hate to see the USAF run the program and have something the largest user doesn't want foisted upon them, an Air Force aircraft adapted (another word for compromised) for the Marines use. The Navy and the F111 come to mind.
Who else in the US military has the experience the Marines do in unconventional aircraft and vertical lift as the Marines? The Harrier 2.0 (F35) experience shows no particular brain trust within the USAF in that direction.
You're correct about the significant power the Commandant can focus on the hill, as evidenced simply by the Osprey's continued existence. I however have to believe the reason the program remains with the Marines is the unique nature of the aircraft, and as you mentioned, the procurement scandals within the USAF.
Perhaps the F35 program should be handed over to the Marines and the RN?