Naofumi is (technically) just a civilian who is initially hated, but gradually becomes beloved by the peasantry and even praised as a true hero while Malty starts out as a princess whose country gradually wisens up to her rotten behavior before being exposed as a manipulative sociopath and stripped of her royal title.
While Naofumi helps as much as he can (albeit with a demand of payment most of the time), Malty seems to actively blight the lives of everyone around her either for her own gain, amusement, or petty spite.
While Naofumi treats his party members like Raphtalia and Firo like his own surrogate family, Malty not only regularly booted out other members of Motoyasu's party without his awareness out of petty jealousy, she also actively plotted to murder her own biological sister Melty (whose just barely older than ten years old, no less!) in cold blood, to the point of trying to burn her alive with fire magic. Bonus points for irony in that its implied Melty sees Naofumi as a protective older sibling instead of (or because of) Malty.
Naofumi fights as a defensive tank with healing and support magic at his disposal while Malty is a fire mage that essentially uses Motoyasu as a meat shield while she hangs back with the rest of his party. While Naofumi also uses fire through his Wrath Shield, it's tempered by the love and care he has for his party while it's obvious that Malty is incapable of feeling such things.
Naofumi's parents gave up on him early for being an otaku and focused on his brother's education, but rewarded him with a higher allowance for helping the latter when he was stressed out. Meanwhile, on top of spending the royal treasury on frivilous things, Malty was spoiled rotten by her father while her mother tried her damnedest to teach her humility as she groomed her younger sibling Melty for the throne. Malty responded by trying to kill the latter during the coup being staged by the Three Heroes church in order to have the throne to herself, only to be stripped of her princess title, renamed Bitch/Bitchie/Whore/Slut (depending on the version), and made to pay off a massive tab as punishment by her mother.
Naofumi was chosen by the Legendary Shield to become the Shield Hero and save the world while Malty is one of many fragments created by a world-destroying goddess to slowly drive the world to ruin.
While Naofumi gets much better after the brutal kick into the dirt given to him near the beginning of the story and eventually gets numerous allies, a harem of his own, and a happy ending out of it, Malty unrepetantly sinks lower and lower with each crime she commits, screws over each and every person she encounters until she has no one left to turn to, and is eventually burned to death like the witch she behaves like.
The party encounters many antagonists that fit the same mold. They are narcissistic megalomaniacs with god complexes. It is even remarked on by Naofumi. This is because the "goddess" Medea has the same personality. These people are either her soul fragments or simply selected as her agents because such personalities are pleasing to her.
Initially they have the most antagonistic relationship among the Four Heroes. They're the opposite of each other.
During their duel, Naofumi initially has the upper hand thanks to judicious use of Orange Balloons, but loses once Malty enters the frame. Their weapons cannot defeat each other, so victory depends on what they bring in support... And Motoyasu's support was simply stronger than a bunch of Balloons.
Once Malty betrays Motoyasu and the Spear Hero gets in a good relationship with the Shield Hero, they quickly become that much stronger, especially in the time-travel spin-off where Motoyasu goes back in time and supports Naofumi. The Unstoppable Force and the Immovable Object have ceased to oppose each other, what else could happen?
In the manga even Malty looks disturbed at how Itsuki treated Rishia. It could be a fragment of a conscience... Or utter disgust at how stupid Itsuki was by throwing away a devoted follower the moment she starts becoming useful because by becoming useful she accidentally made him look bad.
The fact that the Legendary Weapons can't gain experience when near each other makes more sense when you learn the Waves are attacking the whole world. It encourages the Heroes to spread out across the globe to fight the good fight and gain exp that way, granting everyone succor.
The difference between the web novel, manga, and anime are a bit of their own fridge brilliance. As we eventually learn or will learn the concept of a multiverse exists, so any changes are just different realities.
The difference between Naofumi and the other heroes could be compared to that of Roleplayers and more casual players. Naofumi represents those who take the time to learn about the game, getting to know the world, the people in it and exploring everything that it has to offer. The others meanwhile treat it as nothing more than a game, running around and completing quests, but doing nothing to actually invest themselves in it. Treating everyone around them like nameless NPCs who exist only to further their own ends.
The Wrath Shield gives Naofumi access to fire magic and offensive abilities based off of torture devices. What else is known for fire and torture? Hell. Naofumi has been living in his own hell ever since he got to the other world, and the Wrath Shield lets him give whoever he's fighting a taste of the pain and suffering he's been forced to endure.
The fact that Naofumi isn't the first to be falsely accused of rape by Malty comes to mind. We learn in the first chapters that Melromarc is a matriarchy and any harm done on women, even attempting to harm one, is punishable by death. The only reason why Naofumi wasn't executed was because he was one of four heroes needed to deal with the Wave. This means that the men that Malty lied on in the past didn't have the immunity from execution that Naofumi did, and she most likely stole all their money and watched them die for her own amusement. Malty isn't just a serial liar, she's a Serial Killer.
From Fitoria's account, the waves aren't happening only in Melromarc, and every kingdom needed to summon a hero to fight them off. Fitoria's doing everything she can to help, but despite her power, she can't be everywhere at once. How many people died in the other kingdoms during the waves because Melromarc was hogging all four heroes, and because Fitoria was unable to get there in time?