It was just pointed out to us that the characters in the smash melee character select screen that have their portraits slightly lower are exactly the clone characters and no others: Dr. Mario, Falco, Pichu, Roy, Young Link, and Ganondorf, all directly adjacent to the character that they're a clone of.
For some reason this never occurred to us before.
-R
We have previously noticed the difference in vertical position, but thought it was just a stylistic thing for characters on the edges, rather than specifically for the clone characters. It's possible we never put it together because we always thought of Luigi as a clone of Mario when we played, even though the two are actually very different.
-R