My guess would be Factor 5 and my reasons being:
1.) Just how he said it. Matt loves Metroid/Retro and would not doubt their quality.
2.) And factor 5 is known for there visual stunning products...and they had always been able to pump out some of the best visuals for GC.
3.) Also factor 5's game is supposed to be played one handed, which would make me think flying and Kid Icarus. Which plays well that F5's last games have all been flying.
Also i really don't think nintendo holds this franchise that dearly...this will be the first sequel to a game from the NES. My guess it will be a simple game, one hand controller, most likely controlled with IR pointer (think StarFox DS).







