There are some downsides to transferring your DSiWare games to the 3DS. From what I can tell, your save data doesn't transfer along with your games. That's a sad thing for a Cave Story and PictoBits high score junky like myself to discover after the fact.
Still is was more than worth it to transfer my games to the 3DS, if not just for this special Pikmin-based Easter Egg. My precious BlayzeBloo save data may be gone for good, but seeing an army of Pikmin lifting chibi-Ragna's head into the air and transforming it into a gift box is a something I'll cherish forever.
I am a weirdo.