In this case you have to take into account results other than just GTs and monuments along with other podium results. Valverde has been on the podium of Lombardia as well as Amstel. Finished top 10 at Flanders, has record number of wins in several races, and has a lot more wins in general than Nibali.
Yeah, people often forget that Valverde is a contender in almost every race he enters, on almost every terrain, except pan flat. They often forget he has 7 WC medals, a ridiculous achievement! Achieved on various terrains, form rolling to mountain. He came second to Boonen in an 30-40 men sprint, third to Gilbert and Boasson Hagen in an explosive Cauberg finale, and duke it out with the likes of Bardet and Woods on a 20% wall. And at the same time ha has 18

!!! top 10 placings in Grand Tours! Who comes even close to that? I think no one.
Nibali? Yes, a magnificent rider, a legend in his own right, but not as consistent and versatile as Valverde. When he sets his mind on something and hits the right form he can produce miracles, like his San Remo win, and in that regard he's better than Valverde, no doubt about that. But he can't be up there in every race and on every terrain like Bala can, not even close, no one can.
Alaphilippe? Amazing rider already, best in the world right now. In the classics he showed he has the potential to become all-time legend, maybe greater than Valverde. He also, similar to Valverde, has the potential to be a threat in every terrain. In GT's he showed what he can do in this year's Tour, and if he focuses solely on the Grand Tours he could surely snitch at least a podium, if not the win itself. But here's the main difference: he must focus on that! Valverde doesn't need to do that. He just rides... The way Alaphilippe's career is developing I see him winning lots of classics, the big ones, I see him winning a couple of big stage races like Paris-Nice or Pais Vasco, plus lots of stages, but I don't see him winning or podium GT's, unless he makes big shift in his career focus. He just doesn't have that skillset as wide as Valverde has.