the only person I ever suspected of being Zero was actually Akane. As soon as I knew enough about the characters to start piecing things together, she was who I guessed.
Here was my thinking before the true end: Ace was responsible for the experiment. Snake and Clover were in the experiment. Santa's sister was in the experiment. Seven was investigating the experiment. Lotus had two daughters in the experiment, and 9th Man was connected to Ace somehow.
The only people not connected to the others at all were Akane and Junpei. Why were they there? The only explanation I could come up with, as I trusted Junpei to not be hiding things from the player, was that Akane was Zero, as she was the only one with a connection to Junpei.
Of course, it turned out that Akane was very connected and Santa was more connected than I realized, but I was right about why Junpei was there, at least