I think sometimes guitars also change a little over time. It's much more obvious with acoustics, but pickups and things age over time too...
I think too there is just a lot to be said for how a guitar wears in ,feels in the hand over time. The hand will sense those tiny, minor differences that the eye can't see. It's like when you have a favourite pair of shoes, and you buy an identical pair from the same brand a few years later, they'll not be quite the same or feel just quite the same until broken in.
A lot if it is also psychological, imo. I once had the opportunity to play Hendrix's Black Angel, the custom lefty Flying Vee. When I played Purple Haze on it, it felt like that song was just in there. Part of that will doubtless be that Jimi played that number on there so many times, there will be those wear patterns, for want of a better way of putting it, but also - handling a hero's guitar? A mystical object like that? Bound to be something all in the mind with it. I don't even like other flying Vs....