The 13" MBP has a faster GPU by about 50-100% - this helps with games but it can also help with image manipulation software. The CPU is pretty much identical in performance. Both have PCIe SSDs. The MBP supports 4K display output with Thunderbolt 2.
There's a rumor suggesting Apple will introduce a Retina Macbook Air later on this year. If this is true, I actually expect that it will replace both the 13" Pro and Air. But if Apple's plan is to make it fanless, this wouldn't arrive until next year's update.
I personally prefer the MBP design to the Air, the display is much better and it offers more working resolution, which is good for productive tasks. They have some pretty good refurb deals on just now too:
The only difference with those vs new is they might come with signs of use but I've never read any reports suggesting anything significant and they have a full warranty. That one has a 256GB SSD and 8GB of RAM, which are good amounts. A 128GB SSD can get pretty tight for space. The equivalent new would be $1499 and that's $1189 so you'd save $310. You can get the extended warranty on those too for up to 3 years but you can get it up to a year later.
You can get a cheap neoprene case off eBay too to help protect it if it's to be carried in a backpack: