Going by his current track record excluding The Last Story which I haven't played yet, I think it's safe to assume that Sakaguchi leaving SE was probably the best thing to happen to Final Fantasy.
He had a big budget, he made Spirits Within which while not terrible, it could hardly be called a Final Fantasy and couldn't pull in the big bucks. Considering that some of what made it into Spirits Within was part of his original plan for FFVII, I think we dodged a massive bullet.
People say Lost Odyssey's story is great. He didn't actually have anything to do with any of the novellas, arguably the best parts of an otherwise very bland story, which were written by Kiyoshi Shigematsu, or the music, which as we all know was done by Uematsu.