Root was a very compelling entity in the previous season, a mystery just off the screen who entices Finch and piques our interest as viewers. On-screen is an entirely different story. Her defining trait is that she is insane. She plays it well, I'll give her that, but she needs more to continue being a compelling part of the series. Not even the fact that she wanted to free the Machine could save her yet, because it's the obvious goal despite her cryptic means of achieving it.
I enjoy that Reese is struggling to understand the Machine (and that the Machine is struggling to understand someone other than Finch). He's frustrated but he's thinking. He's using resources as he has in the past, but in slightly more productive means. He could not have been successful in this episode if Carter and Fusco didn't know about each other, so good call on finally cluing them in at the end of the season.
And watching Finch train the Machine but not be corrupted by it? Brilliant characterization. Wonderful return of a wonderful series. Let's see what you can do beyond the case of the week.