The problem is that for an adaptation of the Morrison Batman run in particular, the ideal filmmaker for the job would be a David Lynch-type who could seamlessly juggle a wild array of genres back and forth between mystery, Bondian adventure, absurdist humor, melodrama/soap opera and surreal horror. After all, the central thesis of Morrison's run on Batman was exploring the idea of all of the seventy-ish years' worth of Batman lore and comics being canon in some manner or another. So you'd need someone who could pull off something like Twin Peaks for that to be done properly.
Realistically speaking though, there aren't many of those sort of filmmakers out there and likely fewer still who'd be interested or willing to work on a project that's part of a larger cinematic universe where someone else has a more significant hold on creative input in order to abide by the confines of the rest of the cinematic universe.
So practically speaking, we're looking at someone who can at least sell something exciting and fantastical. So whether or not he'd be the best fit for the job, I do think Andy Muschietti is still a very likely candidate for the gig. Especially if The Flash makes insane bank at the box office this summer.