Ares/Mars has been the biggest WW villain, but it's been toned down ever since Perez' run, who gave him a more neutral stance after Gods and Mortals. He needs war, not total destruction. War will happen anyway. He was the voice of reason at the end of War of the Gods.

WML makes him more bad again but Byrne and Jimenez have him as somewhere between bad and neutral, closer to neutral.

Azzarello made him so neutral Diana became him, and then the Finches made it more weird by making Peace her enemy.

Cyborg maybe? Also flash/eobard thawne aka reverse flash/profesor zoom, huh?

^^^ How have DC writers been trying to make Penguin Nightwings main enemy? They rarely interact. As Tupka said, the main crimelord of Bludhaven is Blockbuster. Also, making Penguin his archenemy because Penguin is a second rate Joker, if it were true, sounds like it'd be doing a disservice to Nightwing by making his main enemy just a lower tier Batman villain and not letting Nightwing have his own rogues.

Oh and Red Hood fought Black Mask in Under the Hood when he was still a villain and in the first few issues of Rebirth Red Hood but thats really it. Hes still primarily a Batman villain who has also fought Red Hood, Catwoman and nearly killed Steph.

Alright, yeah, that makes sense. I must've just been thinking about Arkhamverse.

I previously read a Flash comic where Barry had to stop Thawne simply by forgiving him. I haven’t read anything after that.

So wouldn’t that means Thawne isn’t much of a problem for Barry anymore, right?

Flash

“I don’t have a main villain, I like to fight around”

- LEGO Batman

Martian Manhunter's archnemesis is Malefic.

^ true

No, as. I pointed out, many people consider him because he plays an important role in his origins, but the two actually very rarely fight. Out of all of MMs comics, he's only seen in very few and dies pretty immediately after his debut in both universes. In fact, the version in PE was just a construct Jon made to look like his dead brother.