There were things Naruto expected when it came to his birthday. He expected to be chased by a mob (he was). He expected to be beaten by the mob (he was). What he didn't expect was, after he lost conciousness, he would come face to face with someone who looked almost exactly like him but...short.
The difference between Alchemy and "magic" is the fact that Alchemy has a fundamental law. And that Alchemy can be explained by pure and utter science. But that's not the point. The point is that Alchemy has a base to go by while magic is a whim. You can't predict magic, you can't create magic, you can't even explain...