The organization decided it would replace the front office last off season which is why they pursued baseball ops guys like Kenny Williams and Dan Duquette to replace Beeston instead of looking for a guy to just run the business side of things. If I'm the GM in that position, I think I would get the message loud and clear. When the team when on its 2nd half run, the organization had started negotiations with another baseball ops guy in Shapiro, who was said to be looking to get back to into running the everyday baseball ops of a team.
Shapiro will be running the Jays like Friedman, Epstein, Dombrowski and a few others who have the title of team president, but are really the ones running the shows for their respective teams and have a GM who's basically acting like an assistant GM.
I can see AA not wanting to go back to an assistant GM and with the playoff appearance, I can see why he would decide to move on.
It was also reported that the initial offer was for 1 year plus an option.
Anyway, it's really hard for me to understand why so many posters want to get into the blaming game or feel the need to take sides.
What I will take from this is that it's better to be lucky than good because Rogers's first choice was Kenny Williams (another guy who's a team president, but is probably running his team), yet ended up with its 3rd choice, who's clearly the best man for the job, at least out of the 3 that they pursued...lol.