So, I thought about the topic where somebody wanted to play the non-DX version of Link's Awakening.
And I thought... is there any game where you think the GB version would be preferable?
Since Yoshi is on the Ambassador program, Yoshi's Cookie is almost inevitable.
And I realize I'd rather have the Game Boy version over the NES (yes, the SNES version is better, but it's also a third-party game, so we can probably rule that one out.)
For one reason: the GB version has a player-vs-CPU option. You choose one CPU opponent (Yoshi, Peach or Bowser, which I guess is the difficulty select). Or if you had three friends with the game, it supported a 4-player mode.
AFAIK, the NES had no VS. CPU option. And while Nintendo hasn't revealed NES pricing for 3DS VC, it's probably safe to say they'd be pretty close in price.