There's no Shounen in which a early villain is stronger than the last/new one.
Bs
First of all Saint Shanks isnt a villain.
Second of all, this ShOnEn logic has zero weight there is basically no common powerscaling logic accross all shonen.
And yes, there have been Shonen where previous villains still remain the stronger one.
F.ex. Makoto Shishio was Kenshin's strongest challenge even after he beat Enishi. And Oda literally worked with Watsuki as an assistant on Rorouni Kenshin.
WSC Kaidou >~ Saint Shanks.