I think they completely switched places. In the beginning, Yuki was the nice one and Kyo was the rude one, but as the story progressed and they began to become their true selves through their interaction with Tohru, it was like Kyo became kinder and Yuki became ruder.

I mean, in the beginning, Yuki never would have lowered himself to initiating a fight with Kyo while Kyo was only too anxious to fight with Yuki, but after Yuki was the one who got pissed and started beating Kyo up, and Kyo was the one who didn't really want to fight.

I kind of think that's cool, though, that she had them switch places.

I agree. I found myself liking Kyo more and more as the story progressed... it's like... Tohru really humbled him for the better. See, I like stories where your significant other / love interest makes you become a better person -- even better if it's a mutual relationship! (Great, now I'm starting to sound like a biology textbook).