He could...
But a transformation from man to bat-like creature over a matter of minutes doesn't fit with the realistic vibe they've got going. Man-Bat would have to be langstrom's kid, a chimera from birth. It would be a very different kind of movie, about the darkness of the human heart with the purity of youth... on that note, an interesting time to introduce Grayson. After what we've seen, a half-human monster, especially if genetically engineered that way, isn't outside the realm of "possibility" but the transformation sequence is a complete no-go.
The only Batman villain that I can't figure out to make work is full powered Clayface. The dynamic shapeshifting is obviously out of the question, but without it, he's just an arbitrary mud monster. Sandman lite, in fact.
Everyone else, from Man-Bat to Killer Croc to Mister Freeze can be done realistically, even if they aren't worthy of being the central villain.