Trained Pokemon by Rare Candies, haves half power than a Pokemon that been Trained by fighthing. however, there's way to get a Rare Candy Pokemon to his maximum power, like a normal trained Pokemon.

Get the next Items:
Protein
Calcium
Carbos
HP Up
Iron
PP Up (You find this Item in the Secret Dungeon)

Copy these Items and use it on Pokemon on Level 100 or lower.
For each Different Stat Item takes 10 uses on each Pokemon.
Use the PP Up on Each Pokemon's Attack 3 Times.
Your Pokemon will be faster Stronger Defensiver, and also his attacks will be more usefull.