Hi Alex,
I'm not sure what you are proposing - what do you want to prune off, exactly, and how is python-wikitools [1] related to this?
We already have 'a real "pywikipedia core" containing nothing but really needed modules to run basics with personal scripts.' - it's called pywikibot-core ;-). We do package scripts in the scripts/ subdirectory, but they are completely seperate from the base framework.
Alternatively, if you want a smaller framework, there are some alternatives: python-wikitools is one of them, but there's also mwclient [2] and, for instance, Yuvi's python-mwapi, which is really close to the API level.
Best,
Merlijn