I'm pretty sure there was never a plan for Khan to be a reoccurring arch villain. But in Space Seed, he was a dead serious and cunning adversary. There was so much to work with the character, that Bennet and Meyer were able to use him to create the most popular Star Trek movie ever.
I'm certain TNG's producers were aware of this. But despite that knowledge, they failed to create a similar adversary for the TNG crew after 7 seasons of TV. Sure we have the Borg, but they're like the TOS's Klingons. The Borg Queen may be the closest they got. But many people didn't like how that changed the Borg. Q ended up being more of comedic adversary. Bok could have been, due to his desire to get revenge on Picard for killing his son. But he and Ferengi in general became more comedic. I know they were trying to do that in Nemesis, but it didn't work for many reasons.
I'm certain TNG's producers were aware of this. But despite that knowledge, they failed to create a similar adversary for the TNG crew after 7 seasons of TV. Sure we have the Borg, but they're like the TOS's Klingons. The Borg Queen may be the closest they got. But many people didn't like how that changed the Borg. Q ended up being more of comedic adversary. Bok could have been, due to his desire to get revenge on Picard for killing his son. But he and Ferengi in general became more comedic. I know they were trying to do that in Nemesis, but it didn't work for many reasons.