The only problem with that is that the resulting order would be useless for many applications. Say you're looking up your friend Tanaka Tarou, but you're not sure which characters his name is written with. If the sort order is phonetic, you can find the name and likely work out that this is the Tanaka you were looking for. But how do you search for a name in a kanji-indexed list if you don't know the kanji?

Incidentally, this is why kanji dictionaries invariably have multiple indices: one by radical, the other by pronunciation(s).