Think of it as this: Fitz had a magical first half with the Bills - that got him that ridiculous contract. [He was at 5-2] After the contract, he went 1-8. Bills failed to qualify for playoff. With the Jets, he's extended the length - he had one magical season. Now it's his turn to stink it up; good lord Jets didn't give up that 60M contract like the Bills did. After the season, he will know he is at best a backup QB material. Silver lining? There are quite a few; Jets will have a sound drafting position, and Petty did look pretty promising during the preseason. Here's small hoping that either one of them grows up to be a franchise QB.
You may be right, but I hope you're wrong. If you're right, this is just more dysfunction in the Jets' organizational set up. The HC should be the only person making the decision of who starts on the team. Then he lives or dies based on decisions such as these. The GM shouldn't be able to order the HC to play a player because he paid him a lot of money. Everyone makes mistakes. Signings can be logical and seem to be a good move when they are made, but life happens. Sometimes players get old or their skills erode overnight. Sometimes players don't fit into a system or mesh with their teammates. Egos should not enter the picture.
Teams with top QB's have it easy. Any GM with an average signal caller would want some say. Bowles obviously wanted Fitz. back so he has to go with him. We don't know if the GM, coach and owner all wanted Fitz resigned. It would be interesting to know.
I can understand why a GM would want a say in who starts, but if he has personally vetted and hired the HC, then after voicing his opinion, he needs to step back and let the HC make the decision unless or until the HC proves that he isn't capable of making the right decision. The HC works with the team and QB every day in practice. The GM may not be at practice every day. He has other responsibilities and things to think about. At some point, you have to hire someone you trust and then allow them to do their job. Otherwise, it's just a bunch of insecure, ego-driven, dysfunctional mess.
I don't think it's all that serious. The HC and the GM are in constant communication in any organization. When Woody brought in Favre and made Mangini take him that was a mess. This is just normal stuff.