If you know me, you know I've been passionately arguing why there should also be 5.5" iPhone 6s in various threads. So this may come as a surprise… but I think they should put the updated guts in a 4" model too. Why? Because there appears to be a market for smaller-screen phones. So, if it was me, I'd roll out iPhones 6s at 4", 4.7" and 5.5" with updated hardware guts. Those wanting any popular screen size could get what they want, much like there are multiple screen sizes for laptops to suit all tastes/needs/wants.
I've posted the argument that a 4.7" should soak up those wanting a phone screen between about 4" and about 5", and a 5.5" should soak up those wanting a phone screen between about 5" and about 6"… so a 4" version can get those wanting a smaller screen at or below 4". 3 sizes could bite into just about all preferences of phone screen sizes.
Apple has done a good job in the past at poking much fun at sizes above the "perfect" size of 4". There's lots of people actually worried about "one-handed-use" and some worried about "needing pants with bigger pockets". So if that's genuine, make a phone for them too and let the market embrace whatever it wants. Then adapt with the 6s model.
That said though: my gut guess is that Apple is going to roll out new hardware only in the 4.7" and 5.5" sizes. I suspect they are confident that Apple marketing can woo the 4", "one-handed use" crowd into embracing the 4.7" size with little problem.