It was always said that John was the had the business mind in the band. Him leaving could well have been a simple financial decision... Hear me out.
When Freddie was alive the band Queen could command top money for an album, concert, appearance, etc. It could be that after Freddie died and following the Tribute and MIH album concert John just thought the effort to money ratio would not be the same. Why bother getting out of bed and working your arse off if you would be earning a fraction of what you did a decade ago. The fanbase would be smaller without Freddie and so was the amount of money coming in from each album, tour with a Queen+(vocal lead). Yet the effort needed would be the same (or even greater).
He certainly will not need money and I think the financial aspect coupled with Maylor selling out (on a few projects, anyway) he chose to walk away from Queen.