Additionally the A5x was a really expensive chip to produce. It didn't have the graphics power to drive the retina screen so they just threw silicon at it. It had twice the die size as the Tegra 3:

http://www.anandtech.com/show/5685/apple-a5x-die-size-measur...

My money is on them shipping it pretty much for the Lightning connector and beefing the specs up to at least make it look like an upgrade.

that's my guess as well.

I'm not sure how it aligns with previous launches, but I imagined they were going to discontinue the 2 as well.