You don't think I thought of that? It fits the criteria, and it's not like everyone at Intelligent Systems works on the same game. A group could have been split off. It would help explain why Pit is finally getting some attention, too, since Kid Icarus was an Intelligent Systems game. Still, I don't want to get defensive because all I did was suggest a possible answer to the question. Wild speculation can be fun, you know? For example, if I expand the search to non-GC games, I can see that Nintendogs was finished at about that same time. And, much like the Pit connection, there's a Nintendogs connection. Right now I'd say that's the more likely team of the two, in fact.
More speculation! According to Wikipedia, skip Ltd., who developed Chibi Robo for Nintendo, employs some former Square developers. There's also a connection there because Nobuo Uematsu composed the theme music.