I agree with pretty much everything you said.

It would have been much nicer if they stripped out a lot of the dialog, especially when they're describing what is going on. Oh there is a phone ringing behind the wall? I can hear it, you don't need to tell me that the phone is ringing.

Also, you don't need to say that the Machine is saying 9 zeros, I can hear it. Saying it again is redundant and totally unnecessary.

The ending seemed a bit rushed to me. It felt like the writers were trying to stuff as many things as possible into a single episode because it was the season finale.

The Machine talking to Finch at the end (in my opinion) was too overly cheesy, and the Machine's flashy messages seemed really contrived. I think it would have looked better if the Machine communicated through a terminal window (kind of like in LOST when Michael used the terminal to talk to Walt). It would have been easier than animating the flashing message, and it would have been way cooler.

On a slightly more technical note, another thing I noticed was in a previous episode (I can't remember which one off the top of my head) where Root intercepts the information from one of the fiber optic cables running to Samaritan.

I'm pretty sure that if you remove one of the cables from play, then the receiving side (especially if it's a super AI like Samaritan) will be able to detect the missing bits of information that was rerouted. Just imagine you receive 10 folders of the same information for a while, and suddenly, one day, you only get 9. That should set off an alarm.

Even if you took the incoming information and relayed it ahead to the intended receiver, like a man in the middle attack, especially with a fiber optic cable, the receiver would be able to detect the sudden decrease of light being received from the source (because now the light travels through your computer first before going to the intended receiver). The receiver would be able to detect this decrease in light, and know that something is wrong.

I feel like the writers are getting lazy. They seem more interested in putting out an episode rather than focusing on the details and telling a story decently.