These all sound like familiar issues. Last year I started flying in a Sabre Jacket made by 5 11 Tactical. It's designed for law enforcement, but I found it to be very useful when flying.
For one thing it has two large interior breast pockets large enough for folded Sectionals and two exterior chest pockets for sunglasses & a flashlight... And the big selling point was the shoulder pen-holder/pockets. I've never hunted around for a pen since.
It's also pretty simple looking, so you can get away with wearing it anywhere you can wear a windbreaker.
I have a couple of their shirts as well. Also with pen holders in the shoulders.