I suspect that, when Apple get round to releasing the new range, the 13" MacBook Air and the 13" retina MacBook Pro will merge into one, and whether its the "Air" or the "rMBP 13" that has been discontinued will simply be a matter of which name Apple choose.
Even now, its a hard choice between the 13" Air and the 13" rMBP (people are asking here all the time) and, maybe once you get beyond the entry-model Air, the rMBP offers more bang-per-buck. While the rMBP isn't quite as sleek as the Air, its still pretty small and light - a lot of the difference is the visual effect of the taper.
With the lower power Skylake CPUs, smaller combined Thunderbolt/USB-C ports that do everything and the new 'tapered' battery design used in the 12" macBook then - unless Jony Ive has been replaced by an alien pod person - the 13: rMBP is only going to get thinner (and probably tapered).
However, I strongly fear that it will come with just 2 USB-C/TB3 ports and nothing else, because, like it or not, that's kinda the point of USB-C on small-form-factor devices.