I think Girardi is the best long-term option. Dusty's a lot older, and Showalter would be more likely to lose his job under a new front office.
I do still think it's not so great to run things by the owner. Middleton doesn't know anything more about baseball than Giles or Monty did, even if he owns a bigger piece of the club. The real mystery there remains what MacPhail does.
But I don't think there will be any real tension in-season. At the end of the day Klentak still makes the roster (for the most part) and the manager still makes his own calls in-game, even if the numbers say otherwise. You just want them to be on the same page starting out. And Middleton is probably more into analytics than MacPhail, even, which I'm sure is part of why he prefers Girardi to Buck or Dusty.