The only real problem markdown has is the use of () around links, because both of those can be in the link (i.e. http://en.wikipedia.org/wiki/URL_(disambiguation) ). It really should have picked something like <> which can't be in the link itself.
EDIT: the parser on this site seems to think that > is valid in a URL.
EDIT: the parser on this site seems to think that > is valid in a URL.