[Xacual]

Correct me if I'm wrong on this, but didn't we see in the first season that you can edit memories and also implant memories in people. There was that doll that was made to think she was Chiaki in the first two eps of S1. So isn't it possible that Shion's power involves creating things, he used it to create a double of his father and his father used whatever tool it is, maybe another function of ME, to implant as much memories as he could to make it a passable double, and then he and Shion escaped.

So Shion might have created Suou back when he first obtained his power, or its possible he has had his power for even longer but as far as the memories Suou has, she thinks he has only had them two years. Also it might explain why sometimes we don't see Shion in the memories. Maybe those times we don't see Shion are when we truthfully aren't seeing Suou because she had died, and Suou's memories are actually just copied from Shion.