Just to stir the pot a bit. I recently obtained my SID and used the most basic method (get seed, select nature wanted, do taps, get egg) to hatch a shiny egg instead of a regular one. Now, I was also in the middle of IV breeding (without RNG) that Pokemon with the nature I selected. Once I had the shiny in the egg, I spent nearly the entire week resetting for the IVs I wanted, just as if I was hatching more eggs with my parents during the IV breeding process. It was painful, and I likely would have gotten a somewhat better result by straight IV breeding a non-shiny.
Now, I know you can do far more complicated and precise things with the RNG, but all I did was change a legit IV bred Pokemon to a different color. That, to me, could never be considering illegitimate, because the shiny/non-shiny distinction is meaningless other than to look at.
Really arguing about it is silly. All people are doing is approaching perfect IVs. If you work hard at IV breeding yourself, you will still be just fine against them, since you don't need RNG to get near perfect Pokemon. All the other bred members of my team were IV bred the old fashioned way. If you have a well constructed team with high IVs, you are at a slight disadvantage, if any, versus someone who has RNG'd for something closer to perfection.