Stats are not the sole factor in making tiers. For instance, If you were to use that logic, Smeargle would be considered a crappy pokemon if you were to look at just his stats, but you'll notice he's unique in that he can learn any combination of moves you want, making for incredibly diverse strategies.
Thundurus has slightly better typing since the only weakness he gets through his electric weakness is negated through his flying typing. He also has the opportunity for STAB electric attacks, which Tornadus would not get, and in an environment with Kyogre as a driving force, that's a very handy tool to have, not to mention all the flying types present such as Lugia and Ho-oh. Keep in mind Thundurus also has access to nasty plot, which, combined with his prankster ability, quickly makes him a dangerous revenge force, especially if the lead in pokemon has nothing to use on him.
That's not to say that Tornadus is worthless in comparison, since he's still given a subprofile for uber tiers. The tiers are just subjective, and you have every right to disagree with them, so that's just me giving a separate perspective in defense of Smogon.