Elias is living an 'Al Capone' lifestyle in a luxury cell, networking his ass off to continue building his empire. Scarface visits at least once a week with fresh cookies and lots of time for conjugal visits.
Agent Donnelly will ultimately become a supporter of Finch and John, and won't turn John in when he gets the chance to catch him.
The Machine is Finch’s “child” in the sense that it has become sentient, but was infused with all of Finch’s inate goodness and altruism. There will be some rocky times ahead dealing with its teenage years as it tries to learn to comfortably interact with the Team, but nevertheless it will be a force for good, not evil.
Mark F-ing Snow and Root will (or have) come to meet the horrible painful, slow deaths that they deserve.
Finch has replaced Jessica as John's 'one person' who connects him to the world. Ditto for John replacing Grace as Finch’s ‘one person.’
(Many thanks to the terrific
kmmerc for her assistance with many of these wonderful theories!)