Alright, I've just finished playing the game. Here are the answers that I have. Obviously, full ZTD end-game spoilers abound.

• Who/what is Phi ZTD Answer / Theory
• Who is "?" ZTD Answer / Theory
• Where did Kyle go in the mars test site ZTD Answer / Theory
• Who is brother ZTD Answer / Theory
• What is up with Free the Soul/connections to Cradle (I feel there could be more to it than what's already been stated) ZTD Answer / Theory
• What happened to Snake ZTD Answer / Theory
• What happened to Santa ZTD Answer / Theory
• How could Clover and Alice get back to the past ZTD Answer / Theory
• How/with whom did Akane get switched with in first nonary game? (I have a theory that it was intention because of a line that implied that it wasn't random) ZTD Answer / Theory
• How could there be only three survivors of the Mars test site when there are 4 known survivors in vlr, none of whom were the one who stated only 3 survivors ZTD Answer / Theory
• Why do the Zero robes use the free the soul logo on them ZTD Answer / Theory
• Why was Junpei's (or was it Akane's) mental image of All-Ice an identical image to Alice ZTD Answer / Theory
• What is Akane's real plan, since I imagine it's more than just finding a new timeline, since I imagine with enough time she could just find one and I feel that just creating a new timeline would be hollow after Tenmyoji's final words in VLR ZTD Answer / Theory