Trained extremely hard and got in top shape for a guy he thought he would just tool? I don't buy that. I think generally a guy is going to fight like he trains. The slacking will come during the 12+ weeks of preparation, not during the fight. Once you are hit in a fight, the urge to play around with an opponent will most likely stop.
The difference in this fight is that St. Pierre didn't back up. When Serra came in clinching range instead of backing out, St. Pierre used his wrestling skills to take Serra down and pound him. I suppose one can speculate about mindsets, excuses, underestimating opponents, the effects of being in the hometown, etc., but in the end in this fight St. Pierre didn't back out of clinches and that's how he avoided what happened in the first fight. He took Serra down and pounded him when Serra got near (ala gjohnson5's predictions) St. Pierre fought a different fight. Underestimating an opponent doesn't mean you took it easy on him either. It means that he was better than you thought he was.