The message to Shaw.

Was really satisfying seeing her shoot Blackwell.
All the chats with the machine were just wonderful. Gave a lot of insight into her, which has been one of my favourite aspects of the series. They've done a great job really fleshing the machine out as a character as much as any of the human ones. And the pact with John was a nice touch and end for him.
One thing I had expected to be addressed this episode was Root knowing the password for Ice 9 as hinted at last week and confirmed in the commentary. I expected something to come from that, but I suppose that's left to the imagination in the end.
I've had a few issues with this season (Shaw's return should have been an episode all to itself instead of the C-plot to The Voice, Ice 9 needed to be introduced earlier, I have a lot of issues with Synecdoche, Root going to pick up some missiles with the guy from QSO not going anywhere in the end), but it's been a good season overall and it ended on a nice, fittingly hopeful note.
Though, uh...don't we still have mini machine and mini Samaritan sitting in the Faraday cage, safe from the virus? I feel like that should have been mentioned this episode, considering how much dealt with the backup of Samaritan and the machine's core codes. I think that, and some of my other issues like when Ice 9 was introduced, Shaw's return being a C-plot and the missiles leading to nothing probably are a casualty of them finding out late in the game they only got 13 this season, if memory serves I remember them saying they only found out a few weeks before shooting on the premiere. A shame.
Hope this score doesn't take as long as seasons 3 and 4, there are some phenomenal pieces.