Valverde has always been the most naturally gifted out of the two, but has never been the rider that worked the hardest. Neither in races or even in training. It has obviously worked great for him and maybe he wouldnt be as good or had the long career he has had, if he had done it any other way.
He has won many races but maybe he could have won even more if he rode a little bit more aggressive and took some risks at key moments. Maybe he wouldnt have had as many podiums or great placings, but maybe a few more wins. Wins in the races that matters the most, counts more at the end of the day. Thats just how it is.
A majority of his wins has come in smaller races and during a part of his career when the best GC riders didnt target a lot of the one-week races and some lower level one-day races. He has always been good early in the season and won many of those races. Not to say anything is wrong with that, because it is an achievement to always be in good shape and being able to win races, but perhaps some of them were against pretty weak fields and against riders in not very good form. He just never needed much preparation, which goes back to his natural talent. He has always been at a very high level, but could he have reached even more success with actually targeting or preparing "properly" for certain races? Would he had more great wins? Monuments. GTs. Etc.
Maybe doing it differently, he wouldnt become the Valverde we know though. The way he has always ridden has been a part of his identity. His loyalty to the Movistar team staying with them for the whole of his career. Not many riders has stayed at one team for the whole time of their career. They were never really one of the strongest teams and that is something to also take not of. A lot of it has been centered around Valverde. Good and bad.
Then you have Nibali who maybe was never the best rider but more of a hard worker, that has gotten the most out of his ability. Not by just being lucky but perhaps being an overachiever. Taking risks, always fighting hard and never giving up. Even when he was far behind he came back from adversity to be the one standing on top at the end of races. Pulling of great achievements, when nobody thought he could win. Which says a lot about his character.
There are many things to admire about the both of them. I think Nibali has ended up with best palmares and some his biggest wins are more memorable to me, than those many of Valverde.
If the question is "who has the best palmares?". Then it is Nibali, with the GTs and the monuments.
If the conversation is "who was the most talented and the best rider?". Then it is Valverde.