The differences 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 party encounters numerous antagonists that all 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 exact same personality. These people are either her soul fragments, or else simply selected as her agents because such personalities are pleasing to her.
This also partly explains why Malty had nothing else to her character aside from petty sadism, pure spite, a massive sense of self-entitlement, and a complete disregard of the idea how her actions might (inevitably) backfire on her. It's not just that she was basically a copy of Medea in mortal form, she was created specifically to screw over the good guys in any way she could, regardless if she was aware of it or not. Spending the royal treasury on exorbitant things, dicking over the Heroes repeatedly, trying to kill off her own family more than once, helping the local Church fanatics stage a coup twice, etc. In fact, even she might even have been expendable on her creator's part, concerning her own personality regarding her "pawns".
Potentially veering off into Fridge Horror. How much free will does Malty/Myne even have? Is she fully distinct from Medea, a being created in her likeness and sadistic selfishness but capable of her own independent choices or is she less autonomous? Is she some kind of programed being, a simulacrum like pawn, more than a flesh based robot but less than a full independent consciousness? Being what she is, is Malty even capable of good actions were she to desire to do them? Or are they and that desire simply beyond her? Can she physically not help being what she is? Are her actions really all her own or does Medea command at least some of her behavior even while she is totally unaware of it? Does she have freedom to do and choose what she wants or most horrifyingly is she a being incapable of her own independent and moral actions, but otherwise still conscious and capable of suffering? In which case she'd simply be another one of Medea's playthings, something to be tortured for amusement and then abandoned.
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 spinoff 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?
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 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.
Building up on what was said earlier, Naofumi's situation is quite similar to the general player mindset in real-life MMORPG combat. In early game due to the low difficulty, anyone that doesn't have a high DPS is immediately kicked out with tanks and healers undergoing this the most due to their relatively low DPS, as there isn't a need for defense or healing when the boss dies in 2-3 mins. Jump to late game and suddenly you can no longer cheese the raid bosses with overwhelming DPS due to separate boss phases along with many other anti-cheese mechanics, necessitating the tanks and healers that you spent most of the time kicking out from parties. In short, Naofumi is the gamer pro who know the importance of the Damager, Healer, Tank in parties along with figuring out the mechanics bosses will implement first while the others are casual noobs who thinks only blitzing with a high enough DPS is enough against late-game enemies.
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.
It also, unfortunately reinforces the "Devil of the Shield" moniker that he got at one point.
Ren thinks weapon mastery is the best way to make his legendary weapon stronger. This fails because he doesn't take advantage of the stat bonuses granted by copying other swords, thus leaving him with weaker stats than everyone else. Also, since his sword doesn't have alternate forms, his skill set is limited. It will be like a high level character with max skill levels on basic attack skills and not much else.
Itsuki thinks copying stats from weapons is the best way to make his bow stronger. On paper, this is a good method to practice since he can always find weapons from shops and copy their stats to boost his own (like what Naofumi did after being told it was possible). However, he prefers to copy the stats of rare weapons, which indeed have better stats but the fact that they are rare means there's not many of them to go around. Also, the fact that he spends most of his adventuring on things like assisting in revolutions and the like instead of hunting for said rare weapons means he doesn't have too many stat bonuses.
Motoyasu thinks weapon refinement is the best way to make his spear stronger. His idea is probably the closest to that of Naofumi's because his spear, given the right materials, can gain skills or forms that can effectively increase its damage against anything. However, Motoyasu apparently doesn't go out and hunt for refinement materials and spends most of his time goofing off with women, so his weapon doesn't grow as much as it can be.
Finally, all three's refusal to find other ways to strengthen their weapons or develop actual fighting skills stunts their growth even more because of the fact that they've basically been handed the best of their respective weapon types and, thus, don't need to gain any other skills like tactics or self-defense. Therefore, they severely under-perform as the Waves get stronger and they face an opponent who is either a powerful monster or a hero who is superior to them in level and/or fighting ability. Also, as Naofumi finds out, all of their ideas are viable ways to strengthen their weapons, evidenced by the fact that Naofumi has either tried it via experimentation (refinement), practiced it (weapon mastery), or simply being told it was possible (stat copying) and becoming an even more effective hero as a result.
Naofumi and Malty are basically opposites in every way, too.
Naofumi is (technically) just a civilian who is initially hated, but gradually becomes beloved by the peasantry, praised as a true hero, and even given a noble title late in the story. 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 it's implied Melty sees Naofumi as a protective older sibling instead of (or because of) Malty.
Naofumi's party all volunteer (in Raphtalia's case, volunteer after being freed) to become his slaves because of the immense Level Grinding advantage that will help keep them alive, and because Naofumi's too traumatised from Malty's actions to trust anyone who isn't magically bound from lying to or betraying him (any other controls are immediately released). In the first short story from Motoyasu's POV, it's heavily implied (not outright stated only because Motoyasu has a bad case of Love Makes You Dumb) that all the women who join up with his party except Malty and her two friends haven't simply 'decided to seek other opportunities'. Malty has been selling them into slavery, mostly in brothels, because she doesn't want any competition for Motoyasu's 'heart'.
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 frivolous 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 unrepentantly 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.
It's become a meme regarding the apparent uselessness of the Shield Hero when there's a key example of a character from mass-media in real-life who proves beyond any doubt that the shield is a powerful tool and weapon: Captain America. Why did none of the other heroes ever think of Steve Rogers when they accused Naofumi of being useless? Think about it: they don't come from our real-world, they come from alternate versions of it. Captain America—and maybe Marvel Comics and all of our familiar popular culture as a whole—probably don't exist in those worlds.
Theres a caveat that this a meme overlooks the stat-based nature of the setting. It isnt that Naofumi cant attack with his shield. He can. He can attack all the livelong day. The issue is that his attack-stat is so ridiculously weak that he does piddling levels of damage, even if hes smacking his enemy around as hard as he can, with returns that only continue to diminish as his level goes up. Hes forced to rely on allies and counterattack abilities specific to certain acquired shields to do any meaningful damage at all. Captain America would be an example of a shield user who actually has a proper attack-stat. With the RPG mechanics of the setting, and those of the games that inform the other three heroes worldviews, it largely doesnt matter if they have an example of someone like Captain America or not from their own worlds, because its still apples to oranges when it comes to Naofumis situation.
In the anime dub, Naofumi makes a reference to Spider-Man after hearing Itsuki comment that "with great power comes great responsibility," asking if he had been bitten by a spider recently. Itsuki fails to catch the shout out, a hint that Marvel Comics don't exist as we know them in his world.
Itsuki was an Esper who was enrolled in an academy that was training him to better control his powers. Sounds like the Xavier Institute for Gifted Children actually. Could Itsuki actually have been from one of the many Marvel Multiverses where Spider Man didn't exist, or was barely known?
Queen Mirellia's relationship with her daughters, and even her fate was revealed the moment we learned about the magic powers the trio possessed. Mirellia can cast ice spells, Malty uses fire, and Melty favors water magic.
Ice can freeze from water, and can sculpt water into something solid yet powerful and stunning. Mirellia was Melty's primary guardian and selected her to become heir; water and ice are also close elementally. Her mother's guidance, combined with her eye-opening travels with Naofumi, helped mature Melty into the ruler Melromarc needed when she had to ascend the throne at a young age.
Fire melts ice, both can be beautiful to look at, but are powerful and dangerous. The only thing Malty inherited from Mirellia were her looks, while she developed a rotten, sociopathic persona from her father spoiling her. Both mother and eldest daughter were stronger than Melty in terms of magic power, and it was ultimately Malty teaming up with Tact that allowed her to assassinate Mirellia out of spite.
Water extinguishes fire, and with support enough water can put out flames no matter how strong they are. Melty isn't strong enough to defeat Malty in combat alone, but she has actual allies in Filo, Naofumi and his party. Malty never one ups her sister in combat or politics, and Malty getting Mirellia killed only paved the way to Melty to become Melromarc's next queen even faster.
Medea being removed from the adaptations actually has a perfect in-universe excuse: She accidentally hit herself with a retroactive attack at the end of the web novel and the adaptations follow the post-retcon timeline, in which she's already dead.
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 Waves (though the conspirators weren't above hoping he'd get himself killed in them). 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?
While this may sound more like a theory than actual Fridge Logic/Horror. Could the events of Naofumi's Refusal of the Call, actually be a metaphor for death? Strange isn't it that Naofumi was the only one of the 4 Heroes who wasn't already dead? Or was he? The book follows him everywhere, no matter where he turns, and what he does, he can't get rid of it, and it eventually takes over everything in his life, until he finally submits to it. What form of death acts like that? Disease. Could Naofumi have had a terminal illness that was slowly killing him? He even resorts to surgery (burning it), religion (exorcism), even burning it again (experimental and dangerous medication), it takes over his computer, a metaphor that he is searching everywhere online for help, and that the disease is everywhere inside his body now. Finally he gives up and submits to the call of another world (the afterlife). Even worse, what if the disease he contracted was an STD? This would put Malty's betrayal, and Naofumi's rage into a much darker context. If he contracted an STD from a partner who thought he could trust, who might never have warned him, then Malty's betrayal cuts deeper than anyone ever truly realized. A trusted female partner tainted him, and made him a pariah AGAIN, after he came to a new world hoping to start over. Afterwards, his refusal to even associate with any other females without "protection" (slave crests), now makes perfect sense, and what is the best form of protection? Abstinence.
Raphtalias Miss Conception beat in episode 7 of the anime is played for laughs (emphasizing both her unrequited crush and her naïveté despite her adult appearance), However, at first blush it also seems contradictory to her behavior in episode 5, when she angrily retorts to the slave trader that she is too a virgin when he insinuates otherwise. And yet... having been sold into slavery as a child and exposed to at least one extremely cruel owner, its entirely possible that she was made aware (hopefully secondhand through talk) of what can happen to slaves of more depraved masters, without making the connection to pregnancy and childbearing. The fear in her eyes when she first sees Naofumi is not just of whether he might beat her. This also reinforces her later declaration that she knows the accusations surrounding Naofumi arent true, because she is all too aware of what he could have done to her at any time, with impunity, if he really were that kind of person.
Web novel example: Medea attempted to usurp the throne of Melromarc by inserting an aspect of herself as the natural heir's older sister. This plan was only foiled by the queen's insistence on a meritocratic inheritance and some timely intervention preventing Melty's assassination, which would force Malty to be selected by default; how many times has she pulled this gambit off successfully?
The accusation of Naofumi's shield being capable of brainwashing could've been easily disproved if Naofumi decided to do one of these things:
He could've asked the other heroes how he's brainwashing people. Two possible answers to this are through making physical contact with his shield or being under a spell/curse. He can then dare one of the heroes to touch his shield (or any shield he has in his arsenal) or have this spell/curse cast unto them, and then order them to do something they wouldn't willingly do, such as strip naked.
He could also point out that if he has a brainwashing shield, the other heroes should have a brainwashing weapon, since their Legendary Weapons have almost the same skills. Though it turns out that Itsuki does have a brainwashing bow.
If, by some chance, Malty begins to spout nonsense like "your brainwashing won't work on other heroes", Naofumi can dare her to fall under his brainwashing. This would be risky as Malty would probably act like she's brainwashed in order for the accusation to stick, so a better alternative is to dare the other heroes' party members to volunteer as guinea pigs.
All of the above can be dismissed with the argument that Naofumi is intentionally not brainwashing them to prove that he can't, in order to avoid being caught. If people are accusing you of brainwashing, whether you can or can't, your best course of action is to demonstrate that you cannot brainwash them... which is impossible, because there is literally no way to prove you can't do something like that just because you are not doing it right now.
And it needs to be stated that every time Naofumi asked for proof of their allegations, for anything, Malty, Aultcray, or even Motoyasu would simply make something up, with the rest smirking, nodding, and shouting "that's right!" So it shouldn't be a surprise that he got pretty damn tired of arguing his case.