Well, certainly with 6s and the addition of 3D Touch there were more changes internally than just some chips. But, again, even with just some chips and connectors there can certainly be some issues somewhere at times, even just from manufacturing potentially. But beyond that, we are still talking about drivers and software which undergo even more changes with it all (even if the overall UI that the user uses might not seem that much different). So there's something to factor in from that as well.
In terms of paying premium and expecting more and all that, well, there's something to that, although most flagship devices aren't exactly that much cheaper. Expecting somewhat better quality and all that would be within more or less reasonable expectations, but that doesn't exclude some issues here and there, a variety of which have been here and there before as well. Again, it's not unconceivable at all to say that things might be somewhat more worse now that Apple has that much more of a customer base than ever before and more devices in play and all that, and to wish that things would be better. But as far as perfection goes and just the reality of mass production and supporting more and more devices and customers and all that, reality comes into play in quite a large way too.