In particular all the little modes that try to emulate emacs functionality (simple things like rainbow-delimiters or slightly more complex things like undo-tree-mode) are always broken in subtle ways in the "modern" applications. Not to mention all the text navigation features: ace-jump & friends, helm-swoop, etc...!
I guess a large part of this is that emacs has had 40 years to mature and that it was originally written at a time where software was judged on different criteria than it is today.