The only way you can make a ranking that wouldn't make him come out on top of contemporary riders is if you have that as your main goal with your system and then engineer one that favours one of the others.
A system which places overwhelming value on big wins, very little value on small wins and next to no value on good losing results would hardly be one that only someone out to disadvantage Valverde would come up with. I suspect that quite a lot of people would prefer that kind of system. I certainly would.
It’s possible that Valverde might actually end up coming out on top of that kind of ranking due to sheer longevity but it’s not immediately obvious that he would.
He has 6 tier one wins, Froome and Nibali, to name two obvious rivals, have 7 each and their 7 are both considerably more prestigious collections. There’s a very substantial palmares gap between Vuelta-WCRR-LBL(x4) on the one hand and either of Tour(x4)-Giro(x2)-Vuelta or Tour-Giro(x2)-Vuelta-MSR-GdL(x2) on the other.
If you move in to tier two wins, ie GT stages, big one week races, major non-monument one day races, whether he closes that gap at all really depends on (a) how highly you rate Fleche and (b) how much of a discount you place on Vuelta stages versus everything else in this category. I rate Flèche pretty highly but many people don’t at all,
Its only when you leave things that everyone uncontroversially agrees matter behind and start talking about bulk wins of small races and good placings instead that he suddenly has a big advantage. And you can make perfectly reasonable cases for caring or not caring about these.