Hey!
Ok, I think all 3 possible routes to take here are great, and they each have their own pros and cons, so I'll go over each one and tell you what I think:
For #1, I think, as Fireknigh mentioned above me, having someone that has lived through the hardest situations outside the veil and thinks they're the best be introduced to this absolutely insane world could be very engaging and fun to read through. That said, you'd have to know how to make it stand out and not be extremely predictable, as the setup could very easily turn boring if the story is very cliché or predictable.
For #2, this sounds (at least to me) a lot more cult-like, a much stranger/darker tone for this as the children would basically be indoctrinated here. I think this one's got strong potential for evoking feelings of imprisonment/indoctrination and playing with the fact that the Foundation would basically be all these agents have ever known. Now, I don't think this one would work as well in a diary format and may be better told in a different, broader way, so if you're committed to the diary I don't think this is the best choice.
For #3, I think this is an interesting one too, poses cool concepts and great scenes, but, as Crystal mentioned above me, it might detract from the whole "day-in-the-life" thing, and could probably benefit from a broader perspective as opposed to a diary. That said I still think it could work, you'd just have to balance these two themes carefully so that none overshadow the other.
Seeing as most crit you've received has covered similar things, I suggest you take the comments you've gotten and make a concrete choice as to how you'll tell this story so you can continue to flesh it out in detail and receive more focused crit. Hope this helps!
-Phantom out.