I think Showalter should and will win it, absolutely. Mind you, a big key to the O's winning all those extra-inning games has been the incredible work by their bullpen. Just think of all the zeroes those guys have been putting up in the extra innings to allow their team to win.
As far as Francona not winning MOY, or even finishing in the top 3 in voting, I attribute a lot of this to the voters-the writers-often not having a clue who or why to vote for. Because manager is a very intangible position. Often it's the guy whose team improved the most in W-L record from the previous year. That's the easiest way to do it. I did some digging into this and found that for 9 straight years, from 2000 to 2008, the AL MOY was the guy whose team had the biggest increase in wins from the previous year.
Francona inherited a 95-win team with a lot of talent and a big payroll, so it was always going to be hard for him to convince anybody he was a difference-maker.