Yes, Jose has a big edge is OBP and SLG, but consider that Granderson:
1) Has played 9 more games than Jose, who has missed time with minor ailments a couple of times this season
2) Is 24 of 34 stealing bases, which is a bit more valuable than Bautista's 8 of 13
3) Has a huge edge in R+RBI (about 50 over Jose). Some of this is the extra games played and the rest is probably due to the better hitters batting around him. Nevertheless this represents a huge edge in a typical MVP voter's mind.
4) Plays on a team that is playoff bound, while the Jays are not. This has undoubtedly been a factor in past years and I think will be again.
5) As an averagish centerfielder, is worth a bit more in the field than an above average right fielder like Bautista.
I think these two will finish 1-2 in the voting, with Ellsbury, Cano and Verlander also drawing interest.