I suppose this isn't a bug as much as it is a result of improper coding/a questionable design choice but I will consider it a bug as long as keyboards/mice don't do this. The problem is that gamepads aren't recognised after booting the game. Simple as that. This is especially problematic for those with faulty gamepads (as of recently myself), which tend to disconnect. Let's not forget all those times you've been away and you forgot to plug your gamepad before launching. Considering that you guys endorse the use of gamepads (you've recommended me to get one and I did) not to mention that many of you do use them, I really don't see why gamepads don't get the same treatment as keyboards/mice.
If there's some technical limitation that really prevents this, please do tell.