Andrew, nice to see some more activity around this issue. I also have a 2009 Subaru WRX with the iPod integration kit. In order to pass charge to newer devices that require USB power, rather than the FireWire power provided by our deck, you will need something like this:
http://www.amazon.com/Scosche-passPORT-Charging-Adapter-iPhone/dp/B001HN6CVA/ref =pd_sim_sbs_e_1
I have been using every iPhone from the 3G to the 4 sucessfully with the iPod integration kit from Subaru. When the 4s iPhone came out, the deck no longer would recognize my phone and no audio would play. I was never able to find an answer as to why the 4s, even though its just an updated model running the same software as the 4, wouldn't play though the deck.
I just got the iPhone 5 as well and picked up the lightning adapter to give it a try. I am still able to pass power to the phone, using the adapter I mentioned above still, and even got my deck to show as "attached" however I could still not pass any audio to the deck.
My next step is to try this device to play audio over Bluetooth, connected to the integrated iPod adapter with charge converter.
http://www.cablejive.com/products/dockBoss-air.html
I don't anticipate the "skip" steering wheel controls to work, but it would allow the playing of audio without using any cables. I would just then use a USB charger if the phone needed power.
Good luck, and let me know if you find any other options!