Actually, IMO, the main problem is that the context menu works as a dynamic instance - it constantly shifts around, adding and removing options as they are detected as viable.
I think a more static version would be more precise. Consider the static menu of SWAT4 - you point at an object, right-click and a context menu tailored for a specific situation pops up.
What could work in ARMA3 is that the context menu should be generated once on-demand. For example, you point at the helicopter door, press the context menu button (middle mouse button, for example) and a static list is generated, valid for that given situation.
Also, the above proposition isn't anything groundbreaking, it already exists both in Arma 2 and 3 - for opening doors, mounting vehicles, etc - your context action is displayed as an icon. Incorporate the rest of actions into the same solution and you would only have to generate a very short list of 2-3 available commands (open/close door & board/exit).
It works very similarly in Take On Helicopter.
BIS guys and gals, it's time to do away with the old prehistoric context menu which requires you to scroll and re-scroll through hundreds of options. You have cleaned that up greatly in Arma 3, but I think the way forward is a more focused on-demand action menu.