I can totally understand how you feel. As a breeder, I was concerned at first that all my hard work was for naught.
But, if you are a breeder like me that has spent hours, then you probably have the same things I do right now: Multiple studs, several natured dittos, access to multiple of the most common moves for egg moves... With the bank, and your knowledge, you're already set to breed and could do it pretty fast.
I don't think hyper training is going to be as fast as you think, I'd be willing to bet money. I think experienced breeders could make a perfect Pokémon faster than hyper training. You also can't add egg moves, or change natures, get the hidden ability, or do any of that before level 100. It's going to be easier than breeding, but less lucrative and likely more time consuming in the long run, especially if you have to buy/find the bottle caps. If it's BP, for every Pokémon you want to fix, you need multiple bottle caps and will be doing run after run through the tower. It's already confirmed that there are different types,as the Japanese site says that Magearna comes with a 'silver' bottle cap, so there are levels.
No, what hyper training does is give an alternative, simple method that's more time consuming and conditional to up IV's, and even helps breeders fix their event legendaries, shines, etc.
I agree that it doesn't make sense...IV's were supposed to be unchangeable. But, I still think it's for the better even if it doesn't make sense, and I just add it to everything else that doesn't make sense. Like why trading riggers some evolutions, why kangaskhan is born a mother, why incense makes certain Pokémon give birth to the first form, etc. It's dumb, but ultimately a great feature