The problem is that the strongest Pokemon is usually the most used one. Going by W/L you'd have to disregard every match where both parties used the same mon in the team. Which is A LOT of matches. Then take into account that usually people run common cores and this adds to even more disregarded matches. As a result of this you have only W/L rates on teams that don't go against the same suspect in question. This can actually result in the wrong Pokemon having higher win rates since there is less diregarded matches.

Basically if everybody is using OPmon except "trash players" than OPmon has a high winrate against "trash players" but not against the meta. If a majority of people are using StrongMon in addition to OPmon then StrongMon will have a higher winrate due to winning always against "trash players" and sometimes against "meta players". Therefore you move StrongMon to ubers and OPMon overcentralizes the meta.

Usage on the other hand tells you when a meta is oversaturated with a certain Pokemon and that removing it will likely diversify it and make it healthier.