I thought they might do this since it's a higher priced device, like the iPad Pro. I'll be getting the 256GB model, which will be a great upgrade from 128GB.
I think it will be priced $999 for 64GB, $1099 for 256GB, and $1299 for 512GB. Reasoning: The iPad Pro is priced at $649 for 64GB, $749 for 256GB, and $949 for 512GB. The iPad Pro starts at $649, which is $320 more than the iPad which starts at $329. Add $350 to the starting price of the iPhone 7, which is $649, and you get $999. The iPhone 7 Plus goes up to $969 for 256GB. Seems about right to get a premium model for a little more than the top Plus model, but with less storage. I'd think most people already willing to shell out for the premium model will probably go for at least 256GB. I also think starting at $999 is a significant psychological barrier—even if people plan to spend more than that to get a higher capacity. Apple can push that sub-$1000 price point all day long in the ads and other marketing materials and it will be seen as premium but not absurd. Starting prices over $1000 might make many people take pause. But that's just my opinion on the matter.
As for RAM, I was hoping for 4GB like my iPad Pro 10.5" which is blazing fast, but 3GB is probably enough for a phone on iOS. Although considering the rumored price points and potential "Pro" name, it's a little disappointing. Hopefully they'll at least throw us creative types a bone so we can use Apple Pencil with it and use it as a little Moleskine sketchpad that we'll always have in our pockets, but I'm not going to hold my breath.