Based on a client project (XEM 100+ wikis), XWiki has an issue when deleting a user in a farm with a lot of sub-wikis.
If I understood correctly how the process works, when deleting a user, XWiki checks in all wikis if this user is in a group or not. Besides this check, it also checks if the user has rights associated to a document.
Still based on a client project, deleting such user is very long, more than 15 minutes.
Currently the wiki is on 3.5.1.