Also take into account on the javascript redesign, javascript wiki-side extensions.
[[MediaWiki:Common.js]] importScripts [[MediaWiki:Wikiminiatlas.js]], [[MediaWiki:niceGalleries.js]] and [[MediaWiki:buttonForRFA.js]], which then load [[MediaWiki:buttonForRFA/lang.js]]... plus the several Gadgets the user may have enabled.
On Wikimedia Commons I load 38 scripts located at the MediaWiki namespace (plus gen=js). I'm pretty sure loading all of them when they aren't in the cache slows it much more than the organization of the core mediawiki javascript.
Transcluding in the same request files would benefit a lot (either automatically detecting calls to importScript or with a new syntax).
Finally, a dependence you may not have taken into account would be that some CSS from the shared repository should be usable by host wikis when viewing the pages.