As far as I understand, the versioning implementation in OS X is built on top of SQLite, which has one-reader/writer-at-a-time-only transaction semantics. I wonder how much this contributes to the beach balls.

Save As must come back.

iCloud syncing of Notes is broken. Notes which are supposed to be in iCloud often get branched to On My Mac without me noticing, where I continue editing them, only to create conflicts.

TextEdit list view should stay open if you want it.

Notes and TextEdit need to be merged. I like the note browser view, but prefer TextEdit's white background.

A package manager as good as apt-get would be great.