Point one: That's kind of the point I've made. I mean it depends on the person's playstyle. Those who only care for results can play as ruthlessly as they want with all the resources given to them, while those who actually care for their Pokemon on a deeper level (That probably sounds wrong but I can't think of a better way to say that) would never allow their Mons to go through treatment like that. I mean we already got a demonstration of what it might be like, thank you Dr. Sigmund.
As for the other points...alright, I will concede that perhaps for those kind of people who require perfection an option to put it in is not bad. My main gripe, I'd say, is that with the options in it, people will assume you will use them to breed/make a perfect team, regardless of your own opinions on whether or not you want to use said resources for ethical or practical reasons.
I for one simply hope that such manipulation will not end up being necessary for end-game and post-game content. As I've personally maintained, it's much more satisfying to fight, try and win with a team of true friends, with all their quirks and flaws, because it's more personal then just going in with a numerically perfect team.
So yeah, from an ethical perspective I'm against, but from a practical standpoint I can't really say no simply because it's that or hours spent breeding and, if not perfect, abandoning the Pokes. Now that I say that, can't tell if that's even worse. So...yeah, as long as it doesn't become borderline mandatory to use it, then sure, might as well have ways to change IV's slightly.