Unlike auto-complete-mode, Emacs's default completion system is rock-solid. :-) auto-complete uses some pretty messed up popup display library that doesn't play well with many packages. company-mode is much better in this regard.
I guess I'm so used to the default completion system that I don't see it as something primitive and hard to work with. That said, it might not be a bad idea to include a "more modern" completion system in Emacs itself, but I'd opt for simplicity and reliability over fancy UIs.