On the one hand, I like to play through each Pokémon game cold. No ev training, no breeding, no running to Smogon to check tiers. Just me and my pokes, training and evolving together. Don't hack and then breeze through with a level 100 Typhlosion. It's...it's just wrong.
On the other hand, once you've beaten the game and set your sights on wifi battling, feel free to hack, sensibly.
If your game dies and takes your Pokémon with it, you're entitled to take them back.
As long as you don't cheat and make wondertombs, or Machamp with sheer cold, what's the problem?
You could spend forever IV/nature breeding a Cyndaquil, then EV training it, finding TMs, leveling it up, and THEN use it, or you can hack slightly and get exactly the same Pokémon in minutes. There's no difference, and now you can spend more time battling and, y'know, actually having fun.
My point is this:
Using an AR to make Pokes that you could hypothetically make by yourself is fine.
It's just a way to save time.
Using it to make Pokes that have no right existing (Hello, Wondertomb) is absolutely downright wrong.
What you describe isn't so much cheating as it is fast-forwarding.