Question

Why there always a fisherman having six Magikarps in main series Pokemon games?

Answer 1

It's because he knows they'll evolve into Gyarados, and soon everyone will be grovelling at his feet for mercy.

Just kidding.
It's Game Freak's decision, maybe it's as a joke, maybe it's to give the player some free experience or to show them the uselessness of Magikarp. It's what's known as a 'running gag'

Comments

I wish the first part was the answer.

Answer 2

Because Gamefreak likes to use that joke. There is a Japanese stigma about fishermen. It is a cultural gag.