Correct me if I'm wrong but I don't think there are many 2D Marios that feature Yoshi. And none of them are on 3DS. It depends on whether the 3DS eshop has SNES games in it. If it does then you can try Super Mario World. If it doesn't, then you might be out of luck.
There may be a Yoshi game or two on DS if that counts. (since 3DS can play all DS games) But Yoshi is the playable character, not Mario.
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