There are many kinds of "smart".I don't know about strongest but Orochimaru is definitely the smartest of the three.
naruto is an academic idiot, but he is quite smart when it comes about figuring ways to beat his opponent (we have seen that all along the series but specially against Pain).
When it comes to a battle, being a genius researcher, biologist or chemist (like Oro is) doesn't really help you that much.
So being the smartest really doesn't add up much. And besides, oro is no shikamaru (in the sense that you don't see him pulling out a crazy thought out strat to win) he's fighting style is pretty clear: keep a long range and if possible have minions fight for him.