HI, I have the same problem on all phone calls in my Iphone 6S Plus with IOS 9.1. The sound quality from the earspeaker is horrible when making phone calls. I have now already 4th Iphone 6S Plus and they all have had exactly the same issue. First one was tried to be fixed at Apple service. They even changed the earspeaker but no change in the sound quality. I have changed a new SIM card from the same operator, no change. I have tried a SIM card from other operator, no change. It seems to be the problem is not in the earspeaker itself as the voice recorder plays flawless sound via earspeaker. The problem has to be somewhere in the phone functionality - either software or hardware. Both Iphone 5S and 5C do not have any problem with the same SIM card and they have a perfect sound quality.
When I have called Apple support they said they have not heard earlier anything about this problem. It sounds really strange as the sound quality in all of these 4 phones have been identical and below any standard. Many people have been complaining about this since IOS 8.3 in Iphone 6 and the problem still exists in IOS 9.1 with Iphone 6S and 6S Plus. APPLE PLEASE DO SOMETHING!