No matter what, emacs still feels "alien" in my OS's desktop interface with its UI concept, and never fully integrates. That's fine if you don't want it to integrate, but I actually like some concepts of my OS's UI a lot, and miss them in emacs.
And elisp is not a very good language, born of a time where programming languages still had a long way to go (at least in the mainstream, academically it always seems a bit different to me). They are actively trying to fix things, e.g. the adoption of lexical binding, but the scope of this effort also shows how emacs is a very big ship that is hard to change course.
Someone else mentioned lack of proper multi-threading in another comment now, and this is also very noticeable.