OK, let me rephrase cause I see it's quite difficult for people to see past the "just a habit I guess."
Many many players pull the flag just before they hit they ball, I'm guessing these players pretty much do it every time, (unless as stated above, they are trying to use the flag to stop the ball with chips, pitches, etc) which wouldn't be often.
So to make it easier and save a little bit of time, have the option to automatically have the flag pulled as the shot is played. The key word there being option. All it would be is a simple little box to check under options.
Yes, I realize this is not going to revolutionize the way people play, but rather just something small that saves a little time, and yes, in my case forget to pull the flag. I actually use the flag to aim, i.e aim from the default view and not the zoomed in view. Maybe that's why I never got into the habit of pulling the pin, cause I was using it.