[falcowe]

If I had to guess this sounds like either you don’t have enough ram or your single thread performance isn’t good enough (which I really doubt is the case). I would guess the former is far more likely than the latter.
I edit midi on a regular basis in PT like you and I don’t have the issue you describe when clicking on notes to edit them. Even in multiple piano roll tracks at a time. So I don’t believe ProTools is to blame here directly.
As far as deselecting the track, I suspect earlier versions? as you describe you had command focus or something similar setup to follow the focused screen which mean you only at to alt click the track to do the full keyboard shortcut which would be Shift + alt if I’m not mistake to do to all selected. And that should do the behavior you expect (I suspect).
Are you running your VIs in VEPro?