Hmm...
My first reaction was that maybe it's not so bad. As long as you still give a shrinkwrapped game to her, maybe it's excusable if you clearly know that your sister only wants the game and nothing else. Maybe it's reasonable if you are including the game as part of a larger gift package and it's not the main attraction.
But reading more carefully made me change my opinion.
You are proposing that it's acceptable to open someone else's gift and remove all the parts you want before giving the "leftovers" to them? You are assuming she doesn't want the whole package... but don't know that, and still have no qualms about decreasing the value of the package before giving it? You're even planning on opening the actual game and taking out the Club Nintendo code? This game isn't even that expensive to begin with. And no, tossing in a spare classic controller - either used or from an unrelated game - simply because you don't need it doesn't begin to make up for the shadiness.
This all sounds terribly selfish, like something a spoiled child would do instead of a full-grown adult. But maybe your traditions and feelings about Christmas gifts are different than mine.
Do what you want, but since you asked for opinions I don't mind sharing mine. If you really want to keep the goodies for yourself, then it's a much better idea to buy the package and just trade or sell the game disc afterwards. Surely Gamestop will offer good value because it's got Mario in the title.