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Move wikibase stuff to a separate file/module
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It's clear now the question is not whether but how.

The major problem is the backwards compatibility

Probably we can introduce a new Python Namespace for a new model i.e the wikibase file or subfolder to implement a new clean stucture, keeping the old unchangend. Step by step the old implementation can be deprecated and replaced by the new.

See also T108440: Pull out all Wikibase-related parts of pywikibot to pywikibot/wikibase and use it as a submodule.

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We already has a wikibase repository but that didn't work is past because it has no interface to/from pywikibot. Probably it works as a subfolder but I guess it is much more difficult to create a separate module repository to combine with teh Framework. The problem might be to combine it with the data and comm tiers as well as the the page and site level with a new repository. Maybe I am completel wrong.