I have wondered, since most large wikis including all wikimeda projects have these extensions installed, why not make them part of the core?
Topic on Talk:Suggestions for extensions to be integrated
See also Bundling extensions. Note that keeping things modular as extensions isn't bad per se. I can imagine Renameuser might benefit from being completely integrated, whereas Checkuser seems perfectly fine as an extension (doesn't need to be entangled into core). If anything, Checkuser could be bundled, but I don't see a reason for making it a core feature. Only makes it harder to maintain and/or replace for third parties that don't want it.
Checkuser is a vital tool to help, for instance, the maintainer of a wiki (that is whoever techniccally owns it), search for duplicate accounts.
Except for the Wikis that explicitly allow multiple accounts for a single user due to privacy implications. Some even encourage it. Forcing the admin on that wiki to install something which would then need to be manually hacked out of the code is not a great idea.