I think the size of the phone is just a small problem. In my opinion it's the software the needs work. Right now, iOS is just scaled up and that's just not ideal.

For example, take how the Home screen icons stick to the top. You can in theory have 5 rows of icons with a blank one on the bottom. This may have worked well on previous iPhone's but with the iPhone 6 and 6 Plus it makes it even harder to reach.

These are things I hope Apple addresses in iOS 9. Right now it's just scaled up for big phones. It's now time to optimize it.