You don't need a new application for this, you just need some upgrades
to the ZIM generation pipeline. How about sending patches for
https://sourceforge.net/p/kiwix/other/ci/master/tree/mwoffliner to
generate category-based ZIM files and the like?
Customisation possibilities used to be better here before
https://www.mediawiki.org/wiki/Offline_content_generator was deployed on
Wikimedia projects, as ZIM files of few hundreds pages were very easy to
make on wiki. Help with the OCG component is also appreciated.
Finally, icnremental ZIM updates are an area of ongoing work. You can
probably help here as well:
https://phabricator.wikimedia.org/T49406#492033
Nemo