I agree wholeheartedly with you on this. I've always wanted a "standard" New 3DS (ended up buying an XL model just to play Xenoblade). Yet when Nintendo finally brings over the model I want, they do it only in this weird-ass bundle with a game I have no interest in. And to top it off, all combined that bundle ends up costing more than the XL model with the bigger screen.
If I were a cynical cat, I'd say that Nintendo is doing this solely to provide justification.