Apple is all about the average selling price these days: 16GB iPhone they hope no-one buys, 5400RPM HD in the iMac 4K they hope no-one buys, etc. I'm not sure what their plan is with the MBA, but if they want to lure people with a low priced MBA, a step-up to the rMB shouldn't be too big of a jump, or people with just stick with buying MBAs (which are still very popular).
Prices for the rMB:
rMB with 8GB and 256GB: $1299
rMB with 8GB and 512GB: $1599
Obviously these aren't fair comparisons, but assuming the goal is to get people to buy a rMB instead of the MBA:
11" MBA with 4GB and 128GB: $899 + upsell to first "comparable" model: $400
11" MBA with 8GB and 128GB: $999 + $300
11" MBA with 4GB and 256GB: $1099 + $200
11" MBA with 8GB and 256GB: $1199 + $100
13" MBA with 4GB and 128GB: $999 + $300
13" MBA with 8GB and 128GB: $1099 + $200
13" MBA with 4GB and 256GB: $1199 + $100
13" MBA with 8GB and 512GB: $1599 + $0
Once you spec out the MBAs to get close to the rMB, the difference isn't that big anymore. However, most people won't know about those prices, nor care about detailed spec comparisons. They only know about the $899 and $999 starting price, and an upsell of $300-400 is pretty high.
I'm sure Apple has all the math worked out to optimize their profit and ASP as much as possible, but if I had to guess they would make an upsell to a rMB a whole lot easier when they drop the price by $100-200 as suggested. That would move people to the rMB more easily, get more people to use retina screens (customer sat, yay!), and allow them to phase out the MBA line quicker. Maybe remove the higher MBA configs from the lineup altogether and only keep the entry-level models around for a few more years.
Or... Apple's numbers tell them they still make a ton of money on the MBAs and they're perfectly fine keeping the rMB a more premium-priced product for another year or two.
I'm obviously hoping for the first scenario, but wouldn't be surprised at all if the only change we'll see is Skylake, and everything else (including the price, 1 USB-C port, 480p camera, etc.) stays exactly the same for at least another year.