I don't see why the IV change has sparked so much. It's just a more efficient way of doing something pointlessly tedious that takes too much time for many. For me, IV breeding is the reason I quit cartridge battling for the most part.
Hyper training is just a convenient method that will still take hours (albeit extremely less than breeding) since the majority of the time you'll need to raise a Pokemon from level 1 to 100 (egg moves, nature). If you think it devalues breeding, don't use it. If you like it, use it. It's not rocket science, it just makes cartridge battling not a complete frustration.
Hell, despite that this is the ever-competitive Smogon, it's easy to forget that a huge amount of players probably don't know what IVs even ARE. Only once I came into the competitive scene did I even learn up on it. The whole thing is just a favor to competitive players - most of whom aren't thinking "this feels like a cheat code" but "sweet! Now I can actually use my teams without pumping 30 hours into breeding them into existence." Never mind Legendary/Event SR'ing.
tl;dr
Hyper Training is not a big deal unless you're a competitive player; and if you're adverse, don't use it. And can we please quit pretending it impacts the structure of the Pokemon universe's reality? It's a tiny detail even GameFreak probably doesn't seek to justify. believe it or not, the games aren't centered around realism!