Apparently all of pywiki scripts used the same user agent header - Pywikipediabot/1.0, which made it difficult for Wikipedia et al to identify which script used or abused which API features, as well as impossible to contact the author of said script to fix it.
I have recently merged a patch from Ori (WMF dev) to both the main and the rewrite branches. PLEASE UPDATE your pywikipedia code from SVN to automatically start using the new user agent, which will now include the name of the startup script and possibly SVN revision (we might want to switch to a hash-of-main-file based number instead at a later time).
On a separate note, if you are interested in the future of MediaWiki APIv2, take a look at the RFChttp://www.mediawiki.org/wiki/Requests_for_comment/API_Future, and submit your own thoughts on what you might need for your scripts from the next version of the API, or email me directly.
--yurik