Maybe this sounds obvious, but one thing I think people overlook is the fact that the iPhone 6+ is indeed much larger than the iPhone 5/5s... as in, it's much WIDER. The width on previous iPhones has remained constant from the first generation all the way up until this year, so for those of us who have been using it for years, muscle memory has taught us the "correct" position to hold the phone up to our ears to hear the speaker mostly clearly.
Now that it's wider though (especially on the 6+), that same muscle memory is causing most people to hold it to their ear in a slightly incorrect position, resulting in muting of the speaker because it isn't directly over your ear. I imagine that as people get more used to actually using the 6+ as a phone and rebuilding that muscle memory, the issue of not hearing calls correctly will go away.