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Well, given the fact that both pywikipediabot (now officially named Pywikibot) and wikitools are both Python packages meant to interact/interface with MediaWiki, they're... pretty similar. :-)
As in nearly any case, users should use the tool that best fits their needs. Everyone has different hard and soft requirements.
I'm not sure this issue is particularly actionable, though perhaps Alex feels differently. I'd strongly recommend submitting a pull request with improved language for the README if you're interested in pursuing this.
I don't really know enough about the current state of pywiki to really provide more than a superficial comparison. I haven't used it in years, before the rewrite was done. And even then, it had a lot of features I never used.
But I'm always open to people who want to improve the documentation in any way, so if you'd like to submit a pull request, by all means, do so.
and more like this..
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