[Bozos of Bones]

Animatrix isn't anime. Well, not all of it. The Final Flight of the Osiris is entirely CGI, and is packed with more emotion and acting talent than the entire trilogy. I think only half of Animatrix is anime, the rest is in other styles, including CGI.
Your questions will all be answered if you watch the Animatrix shortly after watching the movies and paying attention.
In short:
Neo is a hacker, Morpheus is too but it's impossible to hack into the Matrix, only broadcast inside it.
The Architect is the father of Matrix, the maker of all things inside. Why would it be risky for the machines?
The oracle is the mother of the Matrix. Yes, she went rogue, because she believed humans and machines can live happily ever after.
Smith most definitely took over the Oracle.
Sati? She's a program, created by her father. She is just getting installed into the Matrix as we meet her.
Smith.
Gold angel lights? I honestly have no idea what you're talking abouts. Then again, some moron stole my Matrix DVD collection and I haven't seen the movies in a few months.