Tornadus or Thunderus? i personally think Thunderus is more effective since the Electric Type is very good against a few things from it's high special attack, but thats only my first impression of them both.

Is it even a contest? Who is Uber and who isn't? Thunderus is clearly better with that awesome secondary typing and bigger (albeit still not fantastic) movepool. However. Tornadus is better at setting up rain, especially in UU.

The thing is, "which Pokemon is better" is really a relative thing. Thunderus might be considered "better", but once it's kicked off to Uber Tornadus becomes a formidable foe in OU that can Rock You Like a Specs Hurricane. Aggron is a bajillion times better than Aron, isn't it? Well slap a FEAR strategy on Aron and see it do what the green-eyed Iron Armor Pokemon can't. The list goes on and on - a quick search on YouTube reveals sweeps of all kinds and people beating Ubers with much lower tier Pokemon.
Every Pokemon is usable in its own way, just where and how it's used.

A little tidbit to know after reading that long rant: Yay for my 100th post!

Thunderus, look at all the moves it can learn!

Both of them are pretty scary in their own right.

Thundurus has access to priority T-Wave/Nasty Plot and similar moves, and doesn't have Electric's startling Ground weakness.

On the other hand...Tornadus has the elusive Hurricane to his name, and in the rain, he becomes an absolute monster.

Both of them have their ups and downs, but they're quite different in respect to function. The problem is that Thundurus is in the Uber tier as specified by Smogon, so when in competitive battle you may not have a choice.