The only game you would need to worry about accidentally buying (as of this post) is a physical copy of Xenoblade Chronicles 3D. If you try to buy any New 3DS games from the eshop on a regular 3DS, you will be unable to purchase them on that system.
Other than the SNES VC and a small handful of eshop games (such as Binding of Isaac), you won't be missing out on much.
Edit: Apologies, I forgot to account for online digital purchases from other storefronts. Your best bet would be to use the list provided below just to double/triple check the game you're buying in that case.
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Topic: List Of New 3DS Exclusives?
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