As others have said, it's all relative, but here are some of my observations:
- At best, the 12.9" Pro is at the maximum size for use in an airplane seat (unless flying first class).
- The 12.9" Pro is best used held landscape (YMMV) - I usually draw in portrait and given the space limitations, portrait was not comfortable
- A huge impact to use is the person in front of you. Leaning their seat back or pulling it forward impacts the use of the iPad and the Smart Keyboard (which is a BIG reason I hold the iPad instead of trying to rest it on the seat or tray)
- The size of the people on either side of you can impact usage. I once suffered through a flight where both people on either side of me "overflowed" into my seat - significantly. Beyond other comfort issues, it also limited how much room I had to use the iPad (also I never take a middle seat anymore - it's aisle or window, even if I have to pay for an upgrade).
- There's also very little room to store it during a flight when not in use. I usually keep it in a backpack at my feet, but they don't really want you to do that (they want it under the seat).
In all, the larger iPad can be difficult to travel with. If you travel often, then you'll get used to it. If you travel occasionally, it may be an annoyance every single time.
Having said that, I love having the larger ipad with me for the REST of my trip.
Also of note - it's wonderful on a train!
I've travelled both internationally (twice) and domestically (Eight times) over the past year with the iPad Pro 12.9" and have never been told to stow it. Your mileage may vary, but as long as you're being respectful I don't think they care.