I am on my third phone now. My out of box phone, from AT&T, the blemish was so strong. When reports were coming in, I thought maybe they were going OCD. When I got my phone I was thinking that I won't go looking for it. However I didn't have to. It was not subtle at all. It was an intense spot, lacking light.
This began fading within minutes and hours, days and then it stabilized into a slightly noticeable spot. I called AppleCare about 8 days later. They were aware of the issue, based on their tone of voice, kinda "I know". Usually they would pretend to not know anything and then you would have to explain it to them. They didn't bother asking for any details. They said, if I bought it at AT&T go back and return it there or get it exchanged within the 14 day window. I went to AT&T and of course they had none, and mentioned that they didn't have any since launch day. They said don't worry about 14 days, it's clearly a defect and will be replaced. I said I have an appointment with the Genius Bar a couple of days later, which they said to keep that date and most likely I will have my problem solved much sooner.
I finally went to my Genius Bar appointment at the Apple Store, and they had a replacement ready for me. I checked the screen and the spot was there too. They didn't have any more of my version. They placed an order for a second replacement. They did acknowledge, there was a spot.
This weekend I went in and replaced the phone again, and it too had the spot. The employee, said he didn't see it, but I went to another Apple Store employee and he said he did see it. It seems the spot is more perceptible under certain lighting. For example, at the Apple store, it's slight, but at the mall's food court, it was more noticeable. Also, I checked all the display models, they too had the spot, every single one of them, all colors of the 6S Plus.
I decided to add AppleCare+ to my phone, thinking the spot issue is going to take a while to sort out. The employee said they couldn't do it. I need the original iPhone I purchased. Replacement models can't be entered in the system for AppleCare+. I said, no-one told me that before. I haven't had the phone for two weeks and you tell me this. They said try AppleCare over the phone, which I did and it worked. I got AppleCare added.
I have a case number open, about the spot. I said I will hold on to the phone until the issue is fixed and then I will replace it then. Also AppleCare representative had me post on their feedback form, what I experienced and they should get back to me, if they have anything to ask or tell me.
For what it's worth, this third phone is the best so far. I am thinking if this was my first experience, I would not have noticed. I do notice and when compared to my 6 Plus. I told AppleCare, I can't un-see it, it needs to be taken care of.