If you train your Pokémon yourself by battling with them, your Pokémon will also gain EV points (these increase your Pokémon's stats e.g. Attack and HP). This means that for every level you train your Pokémon, your Pokémon's stats will have increased more, compared to a Pokémon that used a Rare Candy/Daycare Centre/Fitness Centre (unless, you have already reached the Pokémon's maximum EV points, then it makes no difference).
Therefore a Level 20 Pokémon that was trained by battling will typically be stronger than an identical Pokémon that was trained in the Fitness Centre. This is why I think it's fair; you can level Pokémon up easily by paying for it, but it will never be as good as a Pokémon that someone's put lots of time and effort into training.
You can read more about EV points here :)