I think it's pretty clear at this point that he has been thrust into the sort of roles that Sakaguchi and Kitase have played in the past, but there's an utterly crucial difference: he isn't very good at those roles. I think this is evident in both the games he's failed to deliver and the games he's delivered.
He is, obviously, a phenomenal character designer and ideas man. I'm astonished he continues to work in roles beyond this, though, as the continued struggles have indicated he's probably not up to it - too much of a perfectionist, too unwilling to compromise, etc.
Some people are just better off in different roles. I think this is fairly true of somebody like Hiroyuki Ito, too - I think he's most at home designing systems and overseeing gameplay and things, and I think a lot of the pacing problems in FF9 and FF12 (amazing as they are) are probably down to him being more focused there. Somebody who can find the balance is rare (and for my money, Kitase is so far the only one to fairly consistently deliver a balance - even Tabata didn't with FF15). MMOs aside, anyway.
In many ways he is Final Fantasy to them, in that his look and his style has defined the series for the past 20 years now. KH, also, is his baby. So no matter how badly he's fucked things up, he's extremely valuable to Square, and it's in their interests to keep him sweet and keep him from considering leaving the company, to be fair. Versus/15 went wrong under him, but there were extraneous factors outside of Nomura himself, such as his team getting gutted to help fix 13 and 14 as they struggled and stumbled - giving him another shot likely wasn't that big an ask, all things considered. He's very valuable in other ways. For instance, Nomura retains a sort of 'creative control' over his characters, and so he works hard with, say, the products division on how they're used. So if SE Products is doing a new Lightning action figure, he directly feeds back on it, requests changes, signs off on it, etc. He's very deeply embedded in a lot of the business.
(With this said, I predict FF16 won't have a Nomura art style. I think the main lesson from the Versus/15 debacle is that they need to extract the FF brand from the influence of any one creator too heavily.)