It definitely matters because the screen size increase is still pretty meaningful from 11 to 12.9, and the keyboard becomes fully usable instead of slightly cramped.Yeah, but once you hit 11, does it matter anymore? 6 to 11 or 13, yeah, heat and such could be an issue. But 11 to 13 probably doesn't have much difference in heat.
If I could only pick one iPad, I'd pick the 11 for it's jack of all trades nature. Great tablet, good keyboard/laptop style usage, great portability. But since I own both, it's a little unintuitive but I actually use the 12.9" a lot more for the laptop style use cases at home (which is maybe 80% of my usage) and reserve the 11" for the portable and tablet style use cases, which are much rarer for me.