Does Our Organization Really Want to "Help Joe"? Really?
Here's the deal: If we really wanted to help Joe the 1st thing to do is to acknowledge and accept who he is. He will never likely be a top-tier QB by the end of his career. He is a reasonably efficient QB who if put in the right conditions can have 'top-tier' QB games from time to time. I'm still a fan of Joe's, but I think our organization is completely missing the boat on what it would take to elevate his play and make it more consistent. More play makers, coaching continuity and dedication are good, reasonable wishes, but Joe's more important need is urgency. It's mental beyond everything else.
Firstly, have him admit to himself that he's not a top-tier QB currently although he's had a few great games (playoffs and SB). This will only challenge him to work harder to get to that goal and/or humble him enough to know that he must sacrifice enough to help the entire offensive unit to become top-tier. This may mean giving-up some of his salary to procure more talent around him (i.e. - Brady).
Coaching/Continuity: The Marty-thing was a mistake. It won't help Joe to get there at all. The best move would have been to keep Marty as a QB Coach (only). That's adequate continuity. He should have just remained as a season fill-in and continue his earlier role because of his amicable relationship with Joe, but change is needed.
Bring-in a new OC that runs the current system, but lights a fire under Joe and doesn't allow him to dictate his play, scheme or even allow him to over-assess his development. Start with the most difficult variations of the current scheme during the off-season and stay with them.
Lastly, address his ego before it's too late. Yes, Joe has a huge ego. Examples of this are the "I don't want to be lining up at Z and X. I want to line up behind center..." wildcat rant even though the play averaged over 10 yards per attempt, on the ELITE question "I mean, I think I’m the best," he said back then. "I don’t think I’m top-five, I think I’m the best. I don’t think I’d be very successful at my job if I didn’t feel that way. I mean, come on." and his consistent insistence on not audibly out of bad play calls, work with the entire receiving core and skill players during off-seasons and generally not accepting critic even when it's due.
This said, it's mental. If the organization wants to truly help this soon to be 10 year veteran QB and elevate the team as well, challenge is resolve - don't pander to his comfort-zone. He performs better in that role and so does the rest of the team.