Performance, price and battery life are better on the MBA so what's the appeal of the MBP beside HDD?
Right now? It's the expandability by being able to yank out the optical drive and add a second drive for additional internal storage. Apple doesn't support those configurations, though, so it's all DIY, and if you run into issues with your system related to any mod's done to it, you will have to remove those mods before Apple will help you.
There's also the wired ethernet port as well.
Some consider those two things to be extremely important, and as such they carry a lot of weight in their decision making. If you're not concerned about them, then there's not much reason to the get the 13" cMBP these days.
Also, although the 13" MBP processor is clocked higher, it's Ivy Bridge-based (previous gen) so the CPU in the new MBA diminished the performance difference somewhat on that front. In fact (and this is where it gets
really interesting, IMO) the 2.9GHz 13" Retina MBP got a 64bit Geekbench score of 8298, while the latest 1.7 GHz 13" MBA got a score of 8172. This means that talking real-world, you're probably not going to notice a performance difference based on CPU alone.
So, I'd go with the 13" MBA if I needed to buy now and was choosing between those 2 systems.