I think there's a distinction here to be made about whether an application should roll its own authentication (answer: no), whether an organisation should roll its own authentication (answer: probably not), and whether, when we are comparing unified authentication systems which do or could exist, including client certificates, whether client certificates are particularly good (my view: probably not). The question of who designed an authentication scheme, and when and where that scheme is actually enforced (on what machine, in what codebase), are, except in the case of client certificates, largely orthogonal.
(I just wrote up my thoughts on this in more detail and will publish that blog post sometime.)