The neck is number one for me.
The body is a close second... ok, it's a tie.
Like Dave said, p/u's can be swapped, so that's kind of an afterthought.
Visual is getting less important to me as I get older, honestly. Although I'd love to have a decked-out PRS, I love the relic'd thing, too. I won't pay extra for it, I own sandpaper lol.
Actually, I was recently digging on the replacement of the Wolfgangs--the HP specials... custom shop, starting around $2k...

BUT, if they have the same neck as the Wolf... saving my pennies.