One place where I think I can shoot a hole in that comparison is that if Tony Dungy still wanted to be coaching the Colts, he would be. He retired. There was no battle of egos between Dungy and Irsay. With Jones and Johnson, things blew up because they both had huge egos. Jerry wanted the credit and Jimmy was getting it.
A second place where your analogy doesn't fit is that Irsay does not generally stick his nose in day to day football business. He would rather hire a GM who runs football. Jerry Jones IS the GM of the Cowboys.
I think Irsay has completely bungled the PR aspect of the Peyton situation but in the end I think he has done the right thing. The team is old. Fresh ideas were needed in the front office. Peyton's health is in question and he's cost prohibitive. Plus, they now have a chance to draft a franchise QB and string together two franchise QBs in a row which is something that rarely happens in the NFL.
I know that Vol and Colt fans adore Peyton, but the NFL is a business and guys get screwed all the time. In this case Peyton didn't even get screwed... he has a chance to pick his team and go win a Super Bowl, something that Indy was a long way from doing. There is no way that Peyton should've been paid $28 million with Andrew Luck sitting there waiting to be signed. Irsay just needed to do a better job with the PR. He screwed up that part of it. But Irsay is no Jerry Jones.
Well you point out a key difference. Jones was loyal to Aikman well past the time he should have been, and it definiitely hurt the Cowboys. So you're right, there are big differences between Jones and Irsay. I also agree that Irsay does not seem near as egotistical as Jones nor is he his own GM.
Where I disagree is whether what Irsay is doing will be any more successful. historically the Colts took Peyton and started him as a true rookie, took their lumps for a year or two and became a great success as a result.
Irsay wants to reboot on that same idea, but he fired the GM that pulled it off last time, and this is where I see the similarity.
IMO the Colts will not return to the level of succes they had in the Polian-Peyton years for a long time, but ICBW.
I guess we will see.