If anything, I'd think that having an Watch would make the case for the smaller 4.7" iPhone because you're going to rely on the watch for additional functionality rather than having the larger 5.5" phone.
I'm sure there will be may use cases and justifications for any combination.
I'd say it can go either way. You interact with the iPhone less so you can go bigger if you intend it as a replacement for the iPad or smaller if you don't want the extra bulk in your pocket.
Ideally, I'd have the iPhone 6 Plus, so that I can use things like LogMeIn easier, and I could use the Watch to avoid getting the thing in and out of my pocket so much, but the iPhone 6 Plus is just too big in my pocket. Even the regular iPhone 6 is going to be annoying. My pants must be a too tight!
I'd say it can go either way. You interact with the iPhone less so you can go bigger if you intend it as a replacement for the iPad or smaller if you don't want the extra bulk in your pocket.
My plan is to get the plus to do just that! I barely use my iPad anymore, but I occasionally like the functionality, so I am hoping this will be a good compromise.