The usual concern with scrypt is that it has less research behind it. The bcrypt hash function has gone through over twelve years of attempts without being broken in the cryptographic sense. The scrypt hash has only around three years of the same.

I would expect that within 5-10 years, scrypt will be the normal suggestion. It really is much better on the fundamentals, so much so that some experts recommend it even in spite of its relative newness. For the moment, though, there are arguments to be made either way.