I understand him wanting full control of baseball decisions because he had a unique situation with Beeston and essentially did have full control, but there are only 30 (or so) of these jobs in the game and the majority of them do not grant the GM the final say on everything baseball. He had the opportunity to work with and learn from a great baseball guy in Shapiro - he could have seen that as a positive and not an impediment.
I think his ego just got in the way, more than anything. Five year offer to remain the GM of the only pro baseball team in his home country, where he has grown as a professional, where the fans generally love him and he just built a team that went to the ALCS, and he turns it down because Mark Shapiro wants to bounce ideas with his GM and Alex wants to be the big cheese.
smh
Could have accepted but placed something in the contract stating that if a GM offer involving full control of an organization comes up then he is free from his contract with Toronto and able to accept.