I'm not talking just about Fenders, but in general:
1. Better wood. This is not always the case but many older instruments are made with woods that are hard to get and very expensive today, like mahogany or wenge for example. The quality of the maple also seems better in the older ones.
Which older instruments used wenge? By the way, I love my Warmoth wenge neck and its only a few years old.
2. Feel. An old instrument that has been played has a broken-in feel that can't be duplicated by a new instrument. The back of a broken-in neck feels better than anything new.
Ever played an oiled or bare wood neck?
3. Refinement. If the instrument has been cared for by the previous owner(s), the flaws in it have been worked out. It's had a fret dressing and leveling, a better nut installed, shielding added, etc. All of which makes if play better than new.
Big if. Not everyone takes care of their instrument. You should see my used Peavey Fury! Yikes!
4. Sound. Nobody seems to know why but an older instrument just sounds better, all other things being equal. I remember an interview with Steve Harris and he talked about how Fender took his favorite P ("The Blue Bass") into their shop and examined every last detail of it. They built an exact copy, it was even the same weight, and gave it to Steve. He said the new bass looked the same and felt the same but it didn't sound as good.
Besides the fact that good sound is subjective, we have no way of knowing if the tonal difference is due to age or simply that its 2 different pieces of wood.
5. Experience. What M.R. Ogle said! An old instrument brings out feelings in the player that a new one can't.
Cant argue that.