If you are using cloned Pokémon with perfectly legitimate stats and moves to battle with, would you, in the context of the battle, be cheating?
No you wouldn't, you would however be cheating if your Pokémon sported a move it should not be able to learn, for example.
In the context of in-game Pokémon collecting however, cloning is cheating because you are collecting your Pokémon by a use of methods not intended by Game Freak to be possible. They created the game and the rules, and by cloning, you are breaking them. Obviously it's cheating.
Whether it's an issue or not is a totally different question. Personally I don't think it's a problem more than using cheat codes in, say, the Sims is a problem. As long as those you trade with are aware it's a clone, and as long as you're not using your perfect IV clones to gain an upper hand in battle over honest breeders, there really is no problem at all. You're entitled to play the game the way you enjoy it the most as long as you don't interfere with others' experience. There's the GTS though, but oh well.