I thought you lost stat points or EVs or something when you used rare candies? I don't know, maybe I read something wrong. But I've always stuck to the 'Defeat as many trainers and the Elite Four over and over and over again until I have Level 100 Pokemon' Method, so I'm biased.
That's a myth.
What happens in the older games (prior to Gen V) is, once you reach level 100, you cannot gain any more EVs. Using rare candies to level up does not grant any EVs, so naturally Pokemon who gained experience "normally" would have better stats than those who were fed rare candies to level 100.
Now you don't have to worry about that as even if you're level 100, you can still EV train and in XY you can even keep track of your EVs in Super Training.