The new keyboard shortcuts aren't context sensitive enough.
For example, command-A selects all notes in the note list. That seems sensible if I'm in the notes list, but if I'm typing in the Search box, for example, command-A should select all the text in the search box - because that's the expected native behaviour for a text box. But that doesn't happen - even though I'm not even looking at the notes list, command-A selects everything there, and (because the key-presses are swallowed) the search box I'm actually using ignores it.
There are loads of similar little micro-annoyances in the way the keyboard shortcuts have been implemented. They feel more like a hindrance to productivity than an benefit at the moment.