I just re-watched the season finale. Some additional thoughts.
ROOT could be working with Elias or she is rogue CIA since neither Elias' crew nor the CIA were in this episode directly that we know of. It is assumed that when John answers the phone it is The Machine. It could be ROOT. It could be Elias.
Now that Carter and Fusco know about each other, the door is now open for Reese, Zoe Morgan, Carter and Fusco go after ROOT and whomever she is working for to recover Finch. The numbers become secondary at this point. Zoe has the computer skill and connections for intel, Carter and Fusco have the law enforcement research and Reese has the balls to the get the job done.
Next season could be partially or completely on the trail of Finch and his recovery. We all have all said that the number a week thing is a good start, but it can't last as the sole reason for the show. It will get boring. Now, they have set up several plot lines to augment that and it could take the show for several seasons if they decided to not introduce any other plot lines (highly doubtful).
Cool thing is everyone, including the producers and writers are all on the same page with us, the audience. Until next season's episodes are written and produced, no one knows what will happen. That is kinda cool, IMHO.