hmm..
I really enjoy the 250cc class because you really have to ride a smooth line, not that you don't with the other bikes, but if you make a mistake on a 1000cc, it seems easier to get situated again. It seems to me as if theres a little less room for error compared to 600cc as well, the 600cc class is just SO nimble and quick. That being said, I love the 1000+cc b/c being 6'6", thats hopefully what type of bike I'll eventually settle with one day. That raw power is... well, theres nothing like it.
Also, I second what Spectre600 said. It's all dependant upon the situation.
And everyone knows that an advanced rider would kick your @ss at Tsubuka on a 1000cc if your a novice rider on a 600cc.