In 30 years nobody is going to be talking about Nibali, but they will still be talking about Valverde. If there ever was a ''punching above your weight'' achievement, then surely Nibali would win it. Nibali has always stood in the shadow of those who were clearly better than him and he had his greatest wins when those guys were absent. In the meanwhile, generally speaking, you only saw him at the races where he peaked.
Valverde on the other hand was actually one of the best during a long period, be it not so much for GT GC's. Not only was he better at more races, he was also better for a longer period and all year long. You may want to call Valverde a one trick pony, but it has to be one of the more elaborate tricks out there. Being able to climb well enough to follow the real climbers and stay withing striking distance or being able to climb much better than other fast guys. It is no more a one trick pony than GC winners who weren't the absolute best climbers but made up for that in TTs. If it were so trivial as you want to make it sound, then why has it taken so long for others to become better at it? Alaphilippe can't climb nearly as well, for instance. In fact, the first rider to come along that is superior in as well punching as climbing is probably Pogacar.
If you only want to look at their best 10 results i'm sure you could make a strong case for Nibali. However, if you actually watched cycling and not just the list of their best results at big races, and if you value smaller races and riders competing every race they start, then it's not even close. As such, Valverde has made his mark, left a stamp on his generation, while Nibali hasn't, because he will for ever be a guy who won GT's because Froome or Contador or whoever was better at the time, weren't there. Valverde was a generational talent, Nibali wasn't.
It's a bit like comparing Michael Jackson to Prince. If you only take their greatest hits, i'm sure people could be so delusional to think Michael Jackson was the better artist. He only made albums every 4 years, had his best tracks written by Quincy Jones and had the best sound engineers at his disposal. But taking his best 15 tracks, it'd be tough to beat. Meanwhile Prince spat out at least one album per year, has an entire vault of unreleased material, wrote hits (or covers by) for a slew of other artists (Sinead O'Connor, The Bangles, Tom Jones, Alicia Keys, Sheila E, Chaka Khan...) and actually recorded entire albums where he did lead vocal, backing vocals, drums, bass guitar, lead guitar, percussion and wrote and produced his tracks start to finish.