They both seem capable of doing impossable things by punching and are insanely fast and durable. I would say that the Brat of Steel clearly has the edge in mobility, and Popeye probably couldn't move a planet without first ingesting his spinach. Just the same, Popeye is far more unpredictable and is a far more experienced fighter.
Discuss.
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...You are Number Six. Respect Popeye
Punching his head clean off wouldn't so much be Popeye's style, but he might do something like punch him so hard that his cape became Superman bedsheets, his tights Superboy footie-pajamas, and his armor a Superboy Lunchbox that would fall open to reveal Darth Clark's head inside with "X"'s in his eyes.
I think his heatvision is probably SBP's best chance.
__________________
...You are Number Six. Respect Popeye
Popeye eats a single can of spinach and then punches Super boy prime so hard it causes him to separate into Pre-crisis supes , Kon-el and SBP's human form.
Popeye only needs spinach in the cartoon, the comic book version is just a hardboiled badass. He's probably at least as strong as SBP, but Popeye has some high-end matter manipulation. He could just punch SBP to turn him to a toaster.
Heat vison won't hurt Popeye, he's punch back through magic bolts from wizards and fire breath from dragons. Superboy Prime is about a million times faster though. It's going to be hard for Popeye to land a punch, but if he does, Superboy Prime gets transmuted into a crying baby in a crib in a blue diaper.
I say 3 cans of spinach does the job. Maybe 4 cans.
Popeye's family's powers are thought to be semi-magical in nature (another point against SBP), owing to their descent from Hercules and/or a blessing from the Greek gods. In function, he reminds me of Characters in Fables like Bigby Wolf and Boy Blue
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...You are Number Six. Respect Popeye
__________________ I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species that I realized you aren't actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with its surrounding environment, but you humans do not. You move to an area and you multiply, and multiply until every natural resource is consumed. And the only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer of this planet. You are a plague, and we...are the cure.
Well of course, the Vorpal Blade goes "Snicker-Snack!" and it's curtains for whomever's on the receiving end of it. However, Blue is the only Fable sofar with a respect thread as far as I know, so I tossed him out as an example. I think Popeye operates in a similar league.
Now Redcross Knight, there was a swordsman...
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...You are Number Six. Respect Popeye