Many shonen have similar top duos like Luffy-Zoro. And in almost all cases it's the same - one is stronger or at least the only one who can find an extra level against the big baddie.
For example let's take Rurouni Kenshin that Oda worked on as a youth. Kenshin more or less had an equal in Saito and close to equal in Aoshi. But when push came to shove against Shishio only Kenshin could bring him down. Same against Enishi.
That never made me or anyone else feel Saito or Aoshi were weak, on the contrary it just showed how absurdly strong Shishio and Enishi were. Just like Zoro, Law, Kidd, Killer are monsters in their own right but Kaido is the king of the monsters that only Luffy could beat.