The most important “plane” exercises are designed to increase circulation to your feet and legs to prevent deep vein thrombosis (blood clots). You can do simple feet and ankle range of motion exercises sitting in your seat every 20 minutes. Point your toes up and down. Practice writing out the alphabet in the air as if your big toe is a pen. March in place while sitting by raising one knee and then the other toward your chest as this also helps to increase circulation. And be sure to hydrate well.
Getting up and walking in the aisle is important on long flights. Just make sure that you time it so that you get up before the carts come out and block the aisle. When you are standing, raise up and down on your toes to contract your calf muscles. You can also do lunges.
Other range of motion and stretching exercises can be done in your seat as you mentioned to keep your neck, shoulders and back loose. If you really feel like you need more exercise on the plane, you can do armchair push ups, (pushing on the arms of your chair and lifting off of your seat). Or take a resistance band to do some resistance exercises. But the easiest ways not to be bored on long flights is to take a good book, watch movies or sleep. Bon voyage.