I haven't had any problems with my iPad Mini overheating, at all. I've had it for 2 years. In the airplane, it's on the yoke, on this yoke mount:
http://forpilotsonly.com/iPro-Navigator.htm I have flown so far in temps over 100F in the Midwest returning from OSH. You will notice that the iPro Navigator mount is a skeletal mount, so that it doesn't hold in any of the heat, and the flip board does a nice job of shading it, too.
Outside of the airplane, I store the Mini in a padded pouch and never leave it in the sun. Similarly, when I'm using it outside, I only use it in the shade.
As it happens, I run power to the Mini so that it stays charged. Although I agree that when it's been significantly discharged, it will get warm during charging, but if I start with it already pretty much fully charged, it doesn't get appreciably warm at all. Apple claims an 8 hour battery life, but I prefer that the battery is the backup for any power loss.
When I first got the Mini, I had Best Buy install a higher end screen saver, but what annoyed me was the reflections. Then last Fall, I installed a MyGoFlight ArmorGlas anti-glare screen saver, and that took care of the glare without diminishing being able to see the charts. I liked it so much that I installed one on my iPhone 5s, also.
So I highly recommend both of these, the iPro Navigator and the MyGoFlight ArmorGlas anti-glare screen saver.
As far as the Mini itself goes, I'd recommend getting at least the 64 GB size. I only got the 32 GB, and with the other apps I've put on it, it is full enough that when I update Foreflight, it often sends me a message that there's not enough storage. The work-around for that is to delete all of the old downloads first, which opens up the storage for the new downloads. But it would be better to start with enough storage. I'll do that next time, whenever my Mini wears out--although it shows no signs of doing that.
I also chose the cell model, both because of its internal GPS (the non-cell models do not have a GPS and must have an external GPS for the geo referenced map features of Foreflight). For the extra $10/month on my Verizon bill, though, I've really liked being able to connect without wi-fi when I've been traveling. That lets me look at the weather, do emails, web surf, etc., without wi-fi--and I've only come close to my data limit once, when my Marilyn kept hooking up to Facebook on her smartphone while we were driving! She's even less techie than I am and didn't understand the difference between wi-fi and cell data connections.
Cary