Kris,
Both the Mini and the Air 2 will get the job done, and they both work very good in the cockpit. It comes down to your personal preference. I personally used the iPad mini 2 32gb with wifi+cellular.
Regarding memory size, I would go with a 32gb or 64gb. The main app that you will use, Foreflight, will use up at least 10-12gb in itself for all the maps and charts so 16gb is too small if you want to use it for anything else.
Yarden