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There are many, manyways of making the difference between heroes and villains obvious. One of the many tricks consist in making a villain or more wearing armor, while the heroes facing them don't.
One of the main reasons is making said villain a Tin Tyrant, but there may be other possibilities behind it:
The villain's power relies on said armor, forcing the heroes to find a way around to hurt him.
Is a subtle way to imply that the hero is better, because he doesn't need any further protection.
The Saiyans in early Dragon Ball Z wear some sort of armor, as do Freeza's soldiers later, in contrast to the protagonists who mostly wear martial arts gis.
Vegeta in his long transition from villain, to anti-hero, to hero wears less armor every time he gets a costume change, from his first appearance with a battle skirt, winged shoulders, and a scouter, to the Buu saga with no armor at all. Justified since Armor Is Useless anyway.
In One Piece one of the most memorable examples would be Luffy versus the weapon-loving Don Krieg. A good part of the fight revolves around Luffy trying a way to break his armor.
However, Luffy always jumps at the chance to wear armor, believing to be a very manly sort of thing. He even weeps with joy at just getting armored boots and gauntlets from Mr. 3's Wax Wax Fruit during the Impel Down saga.
Yaiba vs Takeshi Onimaru, after the latter is possessed by Fujin.
In Fairy Tail we have most of the guild members against Master Hades, while earlier, we have Sugarboy vs Gray. In the latest arc, the Raven Tail flagbearer (Actually Ivan in disguise) is completely covered in armor.
In Rurouni Kenshin, Fuji at first wears a set of armor as he faces Hiko, but when he's told that wearing it will only boost his confidence and make his attacks weaker, he decides to opt for a fair and square fight, and removes it.
In Gamaran none of the Ogame Ryu members wear protective clothes of sort, while many of their enemies may usually wear chainmail of sorts to protect themselves.
Hanaukyō Maid Tai La Verite. In episode 11 Konoe Tsurugi's Onee-sama wears a heavy armor suit in combat, while her opponents Konoe and Yashima don't.
Though the Seven Deadly Sins, the main protagonists of Nanatsu No Taizai, wore armor in the past, they don't wear such in the present. Instead they prefer to wear relatively casual clothes. In contrast, the antagonistic Holy Knights are practically almost always seen in full armor.
Spider-Man, pretty much an archetypal skintight-suit superhero, periodically though not invariably goes up against armored opponents of various kinds, such as the Rhino or assorted Spider-Slayer robots.
Back when the Silver AgeLex Luthor was sometimes inclined to try brawling with Superman in person, he had a fancy armored warsuit. Superman, of course, had no need for such toys.
The invading aliens from Independence Day have deflector shields on their motherships and fighter craft alike. This renders them invulnerable to Earth's weapons.
Darth Vader in Star Wars. In addition to evoking the look of a Black Knight against the unarmored farmboy, the armor/life support emphasizes his inhumanity.
The Rebel Alliance forces tend to have uniforms with with little more than flak armor, compared to the Empires Stormtroopers who are armored head to toe. Even their pilots are Faceless Mooks.
Played with in The Last Samurai with the armored samurai vs. the modern Japanese army in western uniforms.
In Journey to the West, after starting the eponymous journey with Tripitaka, Sun Wukong wears nothing but a tunic and a tiger pelt used as a kilt, and being monks neither Pigsy or Sandy carry armor. Most of his opponents will show some impressive armors, helmets and plates, usually described in high detail. Of course, that doesn't help them much.
A variant in The Stormlight Archive. While both the Alethi protagonists and the Parshendi antagonists have armor, the Parshendi armor is literally a part of their body. The Alethi just wear armor like normal.
In Doctor Who, the Doctor and his companions are always wearing normal Earthly clothing, while monsters like the Daleks and the Cybermen are heavily armored.
Warhammer 40K: Both Space Marines and Chaos Space Marines use armor, but the CSM's is the Obviously Evil kind, decorated with skulls and spikes and sometimes demonically possessed. By contrast, the Imperial Guard has flak armor, referred to in fandom as "T-shirts" to emphasize just how badly the Guard is equipped.
In God of War we have Kratos, who's almost always wearing a loincloth and sandals against the heavily armored Ares. The third game pit you against two notable armored bosses: Poseidon and Hercules. In both cases you have to smash the armor first.
Jack versus the Big Daddies in BioShock 1. Jack is wearing a casual sweater, while the Big Daddies don't look human because all you can see is armor. Justified as Jack is the Right Man in the Wrong Place and gains more health thanks to 'Adam', while Big Daddies were designed to survive bullets.
Inverted in BioShock 2. Subject Delta IS a proto-type Big Daddy, while the splicers are just crazy humans.
Booker versus almost anything in BioShock Infinite; The Handymen are disabled men now in Mecha-suits, the Firemen are permanently trapped inside their suits of armor, the Motorized Patriots are completely made of metal, and various soldiers have heavy battle armor. Booker, on the other hand, relies completely on an invisible magnetic shield around his body.
Golbez of Final Fantasy IV is a Tin Tyrant, while only two out of the twelve members of the player party are armored (Cecil and Kain). Cecil also loses some armor coverage when he transforms into a Paladin, although he's still clearly a knight.
Exdeath from Final Fantasy V, in wizard form, wears a pale blue armor with gold trims. The Light Warriors do have several heavy armor jobs, but their Freelancer outfits (which they're liable to fight the final battle in) are just clothes.
In Final Fantasy XII, the main party are wayward members of La Résistance who spend a good chunk of the game fighting Archadian Judges, powerful warriors armored head-to-toe to enforce the will of the Empire. The main party sticks to normal clothing, which only includes a couple of token armor pieces if any.
Legend of Zelda games: except in a few games, Link is always facing enemies dressed only in a tunic and pants. His armored enemies range from stone statues to ten-foot-tall knights wearing full plate. Later games would add a thin chain or scale mail shirt under the tunic, however.
In the Castlevania series, heroes rarely wear armor at all, while, among various things, living armors are recurring enemies, in one form or another.
The robot probe sent by Gallaxhar in Monsters vs. Aliens has deflector shields that render it invulnerable to the Army's weapons. The five monsters battle the robot without armor or even weapons. Ginormica puts up a goodly tussle, and Doctor Cockroach is, of course, unkillable.
Inverted with the armored conscripts that defend Imperial China from the armorless Mongol horde in Walt Disney Pictures' Mulan.
The Urpneys from The Dreamstone wear metal armor and helmets (they also wear swords on their belts that are never used in combat). The Noops Rufus and Amberley are completely unarmed children (though Rufus has a similarly underutilized sword in the first season) and the magic powered Wuts are completely naked. Both of the latter groups suffer much less to slapstick injuries than the Urpneys despite their armor.
Ben 10 versus the Forever Knights. Ben transforms into different aliens, but none of them really have armor. Gwen and Kevin count in the sequels. Kind of.
Teenage Mutant Ninja Turtles: The Ninja Turtles only have shells, and many of their allies are completely unarmored, but Shredder is heavily armored. Especially so in his 2003 incarnation, where he is clad from head to toe in armor.