You raise a good point, but one that's probably an issue to a minority of those implementing applications that require an authentication component. Sure, the Twitbooks, GooSofts and FaceLinks of the world that deal with large numbers of concurrent authentications have to think a bit more about this, and that's fine; I would expect that they would be well equipped to do so, and likely also run dedicated authentication servers and carefully considered systems.

I can probably count on one hand the number of times I've seen an application use bcrypt or scrypt and define their work factors. The common case seems to be sticking to the defaults that their chosen library ships with. While these may be somewhat less than ideal, it's universally true that these schemes are stronger than salted passwords fed to a fast cryptographic hash.