I'd go with the 64GB 3rd gen iPad - that's what I went with when I bought my DL and no regrets (other than general annoyance about IOS way of doing things)
I'm only using about 16GB of it now, but for every computer I've owned in the past 20 years, I've always bought as much memory as I could afford and its always full within a few years. I doubt this will be any different.
I went with the 30 pin interface because there are more 3rd party devices that support it and 3rd gen was significantly cheaper than the 4th Gen for same memory. Dont forget to count the cost of the adapter. Also, from the bit I have read about the lightning interface, it is cool from a technical perspective and being able to flip the orientation of the plug is nice, but it seems like the main reason Apple went with it was to have more control over 3rd party devices. That could backfire if Apple tries to get too big a bite from 3rd party mfgs and 3rd party mfgs start looking at Android or Win8 tablets as the flagship hardware interface.