I often use ctrl+p and wonder why the subdirectory links appear before the links in the root project folder. The other way around seems a bit more logical to me.
Actually, in an ideal world the results of ctrl+p would promote the priority of items that are directory neighbours to the file you are currently editing, with the rest of the results being ordered in the usual, predictable, alphanumeric way. That's imho. There's a million ways you could order them and the current is, at least, very predictable