Yoshii confirmed to be an Easter egg for the Metal Gear Solid 3D: Snake Eater game. It would make it the 2nd MGS game in a row on a Nintendo platform the dinosaur has appeared in with Twin Snakes being the first.
Most likely he is just going to replace the hidden toy frogs in the game but Konami as a joke didn't deny it wasn't possible to eat him.
Also not answered is what happens to the 3D effect later in the game due to something happening to Snake in the original version
he looses sight in 1 eye which could be used to disable or alter the 3D effect for that part of the game
http://kotaku.com/5810150/can-snake-...wouldnt-answer