I think a great candidate for Manager is Roy Halladay. He is exceedingly smart, understands the game very well and has the respect- if not the fear- of the players.
I was watching his interview with Stephen Brunt, and he said something quite telling. While the Jays teams of the early 2000s definitely had enough talent to make the playoffs and do some serious damage (the 2006 team especially), he could never put his finger on why they never won a Division or Wild Card. When he went to Philadelphia he instantly diagnosed the problem. In Philly, they expected to win, while in Toronto they just hoped to win. I strongly believe that this thought process is still prevalent in the organization.
I am convinced that Halladay has the skills and knowledge to be an excellent Manager for the team, and most importantly he could hopefully provide the intangible of bringing an expectation of winning back to Toronto, like we had in the late 80s and early 90s.