During my short time of working with the mediawiki api I have come up against what I see as issues/bugs.
When I have asked that we rectify I have frequently encountered the response "we can't change this as that might break backwards compatibility"
I therefore think a versioning mechanism for the api would allow us to make these big changes without fear of disrupting existing users of the api.
This could be done via a query string parameter or separate url
i.e.
http://en.wikipedia.org/w/2/api.php
http://en.wikipedia.org/w/2.4/api.php
OR
http://en.wikipedia.org/w/api-2.php
http://en.wikipedia.org/w/api-2.4.php
OR
{insert naming scheme here}
Version: unspecified
Severity: enhancement