>so who's in charge? Just the Arcitect?

The agents are just extensions of the "mother", programs that take over when necessary to maintain the status quo.

>not given Neo
>the choice to save Trinity, and just let everything reset
>because Smith would pose such a danger as a free-roaming
>virus?

Artificial intelligence cannot control or predict choice. There is no real logic in human emotion. Agent Smith, as a virus, can be scnned and cleaned up/removed but not the emotional aspect of humanity and that's what I think that whole monologue in that room was about. You can only control someone if you can predict their actions.

>But, if Smith can retain the attributes of humans, and thus
>was able to be drawn into the "real world," wouldn't he be
>capable of dying? I again, don't understand how an Agent can
>bleed/be human and Not be mortal. And, since Zion is likely
>part of the Matrix, he would just still be capable of his
>Agentpowers inside of the real world/Zion.

In Reloaded, Agent Smith did say that something happened when Neo went into him, he changed. His abilities evolved and perhaps thats what allows him to appear human. I agree that the bleeding is unexplainable but I think I know why he cut himself.