One could possibly design a new wiki system as a pass-through layer, with MW as a back end and with functionality being migrated forwards into the new system over time as people got used to it.
I think there's an opportunity either for a reconceptualized enterprise oriented MW like system, but done in a clean sheet project and partly or entirely outside the Wikimedia Foundation, or for such a project as a passthrough layer intended to eventually replace MW and done within the Foundation. Whether either of these will ever happen I don't know. The most common Wikis seem to be MediaWiki (with all its warts), Twiki (with all its lack of functionality and administrative warts), and SharePoint (*cough*gack* - though I use it, too). None of these is optimal for the typical wiki environment, users or administrators. We seem to be muddling through.
Isn't this what Mindtouch Deki did? Deki is/was a fork of MediaWiki.
http://en.wikipedia.org/wiki/MindTouch_Deki
Confluence is also a fairly heavily used enterprise wiki.
Respectfully,
Ryan Lane