Alongside his physical attributes which meant he was one of few players in the literal history of the game who could go toe-to-toe with pre-injury Ronaldo, Nesta's reading of the game was impeccable no matter the system played, partners paired with or type of player he was up against. He had numerous injuries as he aged, so was stripped of the gifts that made him the physical match of any type of forward, and that's when he displayed his intuitive understanding of positioning, spatial principles and how an old wizard goes about modifying his game with a large amount of his pace and agility stripped. Him putting on a performance for the ages against peak Messi, at an age when he really should have been retired, cemented that part of his legacy, because that Messi vs that Nesta was supposed to be a showcase for the former and it ended up being the opposite.
For me, in a literal all-time xi vs Mars or what have you, he's my CB and the position next to him is up for grabs; there's no type of opponent I'd doubt him against, from the small, nimble types (who Rio did not do so/as well against, but we're talking criticism of the elite here, so amongst that non-elite tier, you'd not even put that out as a criticism, but in the all-time stakes, you micro analyse every aspect to separate these guys) to the large, physically intimidating opponents, who again, Rio was not at his very best against - which is where Vidic was invaluable - Nesta's enemy was his own body rather than any type of forward.
In terms of intuitive understanding of defensive play, I'd only have Baresi above Nesta, as, for me, he's the best of all-time in that regard, but if we're ranking each aspect of a defender out of a 100, I'm pretty certain Nesta trumps everyone in terms of being the complete defender. I've always put forward in discussions about this that you put a large, powerful, preferably pacey striker on Baresi and he'll automatically need help, same for Rio with certain types of player; it's the likes of Nesta, Figueroa, Kohler and I'd like to say prime Maldini (but he was full-back then, so not really in this discussion) who that's not the case for, which is why they're the ones jousting for best centre-back, for me.
By the way, this isn't a slight on Rio; he was a magnificent centreback at his best, it's just that we're talking about the best centrebacks to have ever played the game, which is just another kettle of fish - if someone said Rio was the best centreback of all time, they wouldn't be taken seriously, as opposed to Nesta, who is always in the conversation with the aforementioned in this post.