We had five great seasons of Person of Interest. All the way through we were shown how the Machine learned to mine the data it received, all the CCTV, the audio, the emails and other digital documents it had access to. When Samaritan was taken online and then was made a permanent fixture after the trial period, I believe it would have been best for us to have been given a second Machine and for us to see Harold, Root and a few others working together to code it and do all of the tests to ensure it was as good as the primary Machine.
The reason for this is because Samaritan was essentially OP in the way it had access to everything and was able to see all, and the Machine may have been able to hide the good guys with new identities and encrypted communications on a private network, it still seemed to have meant that Samaritan had quietened the Machine (in season 4 it hardly spoke to Root) which never used the hidden network created for the Brotherhood and piggybacked upon by Team Machine. A new Machine (M2) would be an ally to the original Machine (M1) by using private networks created all over the US and could communicate with Team Machine using VOIP phones over those networks and share all intelligence gathered from external sources with Team Machine and give them access to what would be essentially a new version of the Internet for their use only. Their phones, their laptops, anything they owned would only be connected to this network. And M2 would run simulations, modelling various situations and advising Team Machine on best options for dealing with threats.
I do understand why the writers wanted the Machine v Samaritan as it’s God v God but logically there should have been another ally for Team Machine and because it would take a lot of time to recreate the Machine, this would take it to near the end of the series so it would be taken online and immediately start building new networks and aiding Team Machine thus putting more pressure on Samaritan as Team Machine started to use different tactics and the Machine’s strength would be bolstered by this new entity – it’s clone, or sibling, whichever way you wish to look at it. I did love the Machine calling Harold father, that was really cool, and very very sad at the same time given what it said afterwards – and both would win the fight and possibly kept from each other so they don’t end up trying to fight each other later on.