However, wiki-markup has no convenient way of representing footnotes and citations.
Not only wiki markup: Footnotes aren't easy to display and to use with html pages and computer screens. PSs aren't useful anymore in e-mails, as one can edit inside the text (what wasn't possible in hand written letters). I guess that footnotes go the same way: they aren't useful anymore, as additional info can be added inside the text itself or simply linked on.
If I do recall well, inline external links are bad because their targets can change after a while and become obsolete. In a perfect world, citations wouldn't point on, say, a newspaper article, but on a cached copy, or on some archiving (and trusted) web-site, and not only carry an URI, but a date. On wiki editor pov, this could be done simply by coding like this:
As Untel said in LA Time, "bla bla bla" [[Citation:http://blabla.bla]]
After edit, the thing could become [[Citation 11/1/2004:http://blabla.bla]], will simply display as [1], and would be a link on whether the cached page or the original one (maybe depending on whatever the original page has been modified or not). I don't know if wikipedia could handle the caching of those pages, but I suppose this to be legal, as google already does.
(Only a little idea poping in my head)