Adaptation Displacement: Almost all the canon nowadays comes from the Filmation animated series, instead of the original pack-in mini-comics. Even the mini-comics themselves began adapting their own canon to fit with the cartoon.
Alternate Character Interpretation: Is Webstor a Well-Intentioned Extremist who wants what's best for his race but still doesn't approve of them torturing prey, and seeks to rule Eternia to find a compromise, or just a power-mad villain who sees the world as a buffet? Is Whiplash a Nice Guy who was forced to team up with Kraal for his own purposes and genuinely regrets all those human sacrifices, or a black-hearted monster consumed by hatred for his damn brother? Is Beastman a Woobie whose intelligence was destroyed by Skeletor's torture, or an animal abusing Jerkass? Is Trap-Jaw a typical Snake Mountain dumbass, or the Only Sane Man who Skeletor horribly disfigured when he attempted a rebellion? Was Keldor denied his birthright to the throne out of pure racism against the Gar, or was he digging into secret dark magic at an early age to conquer Eternia?
Horde Prime. Some find him a cool and compelling villain, while others feel that it diminishes Hordak's importance if he's not the leader of the Horde.
Creator's Pet: Mighty Spector, the character created by Scott Neitlich for MOTU Classics. Also Whiplash, in the original series. He gets the most screen time of any second season villain in the Filmation cartoon, and arguably has the most developed character as well, next to Evil-Lyn and Skeletor of course.
In "Prince Adam No More", Skeletor made Beast Man fall through a trap door. Think about it while remembering Spin-Off series She-Ra: Princess of Power would later establish Hordak as someone who usually does this to his subordinates and was the one who used Snake Mountain as headquarters before Skeletor.
He-Man was redesigned with less of an accidental Hard Gay look to him for the 2002 reboot. Who did they get to voice him? Openly gay voice actor Cam Clarke.
Prince Adam is quiet and unassuming, wears pink, has a secret he can't tell anyone, has only one female friend and is strictly platonic with her, likes cats, and transforms into a tanned body-builder in leather and loin-cloth by waving around a phallic object. He spends his time hanging around other body builders in similarly revealing clothing, and fighting even more bodybuilders in skimpy outfits.
"By the power of G(r)ayskull!"
Characters named Ram-Man and Fisto. Fisto.
It doesn't help that Prince Adam in the 2002 series was voiced by the openly gay Cam Clarke.
All that manly facial hair...
I Love the 80s lampooned this subtext in its review of MOTU, with clips of Prince Adam talking about protecting his "secret" interspersed with suggestively looping footage of Beast-Man grappling He-Man from behind.
The New Adventures of He-Man almost seemed to embrace this, by changing He-Man's outfit to be tights and a leather strap across his chest, giving him a ponytail, and having Adam speak with a pronounced lisp. Adam also has what can only be pigtails.
This article about the live-action film. According to it, Skeletor and He-Man are bitter ex-lovers, with He-Man accepting his gayness and proud of it, while Skeletor is ashamed of it, in a self-deluding relationship with Evil-Lyn, and intent on punishing the true object of his desire for tempting him.
Given his constant humiliating defeats, it gets hard not to feel bad for Skeletor at times. The writers even did several episodes where He-Man and Skeletor team up because that was the only way they got to let Skeletor win.
A case could be made for some other villains, especially Mer-man, who once tried to sacrifice Teela, but is generally hated by every other member of Skeletor's team (and there was also an embarassing incident with a perverted octopus once, in "Prince Adam No More..). Trap-jaw is basically a straight-up Jerkass, while Tri-klops and Beast-man are just plain Woobies. The former was never a jerk to begin with, and the latter is only a jerk if you believe the backstory given in the series bible. The German episodes, in fact, make poor Beast-man downright pitiable.
When Skeletor and Beast-Man are flying around turning things to stone, Man-at-arms stands up to them and shouts, 'YOU DON'T SCARE ME!' while firing his blaster at their ship. This is supposed to be dramatic?
No Yay: Quite a few people like to pair He-Man up with Skeletor, unaware that he's Prince Adam's uncle.
Older Than They Think: It's commonly alleged that the idea of giving He-Man a secret identity as Prince Adam was made up for the original animated series. While it is true that He-Man was just He-Man all the time in the earliest mini-comics, it's also true that Adam originated in DC Comics's short-lived Masters series that predated the cartoon.
Poor Man's Substitute: Serpenators are this to dragons. King Hss accuses He-Man of being one to King Grayskull, and he's kind of right despite the tropes used to describe him.
Replacement Scrappy: Sir Laser-Lot gets an extra strike against him for succeeding Man-At-Arms in the official continuity. Unsurprisingly, not everyone was happy with one of the original eight characters of the franchise being Killed Off for Real and replaced by a never-before-seen nobody. To make matters worse, there were pre-existing characters (like Fisto or Clamp Champ) who had already been established as being the people directly under Duncan in the hierarchy of the Eternian military.
Rescued from the Scrappy Heap: Bow; his new action figure, which is in scale with the rest of the Masters of the Universe line and show accurate head (complete with mustache) has helped soothed a lot of complaints about him and his original figure.
Rooting for the Empire: Quite a few people root for Skeletor and the Evil Warriors. Hell, even the writers of the Filmation series felt bad for them and did some Enemy Mine episodes just so Skeletor could actually win for once.
The four scientists of Primus are the collective Scrappy of the New Adventures. Alcon and Gepple are somewhat tolerable when not along the rest, but the other two are never anything else than their bickering, bumbling selves.
In the Classics line, the Mighty Spector, and to a lesser degree Sir Laser-Lot, have received quite a bit of vitriol from fans who feel that they have bland, uninspired character designs (the idea that they look more like comic-book superheroes than science-fantasy characters is brought up a lot) and that they don't fit in with pre-existing characters. Not to mention, both have been given quite important roles in multiple eras of the canon, thanks to Spector's time travel (which is itself a source of great controversy).
So Bad, It's Good: The original cartoon. The 2002 series is much better, though it still has its moments.
They Wasted a Perfectly Good Plot: Season 2 of the 2002 series saw the formal introduction of the Snake Men, who were also bent on conquering Eternia. They battled He-Man and the Masters often, but despite being a rival faction, they had no real interaction with Skeletor's Evil Warriors. Their only clash was in "Rise of the Snake Men, Part 1" - a battle some saw as disappointing due to the Snake Men curb stomping the Evil Warriors (who had already been wearied from battle with the Masters). (Reportedly, the unproduced 40th episode would've seen Skeletor leading an offensive against what was left of their ranks.)
Webstor, Modulok, Spikor, and Mantenna from Filmation's He-Man and She-Ra, respectively, count. Why are there so many goddam cute villains in the Filmation versions of these shows anyway?!!
Uncanny Valley: Due to a lot of animation involving rotoscoping motions, such as Beast Man charging the camera or He-Man lifting a rock, look very strange as though the motion is both too fast and too slow.
The up-beat theme when Skeletor is around are equally good because they encapsulate his personality. They ham up the scenes as much as him.
Ensemble Dark Horse: Skeletor was the film's resident scene stealer, but Evil-Lyn has a fair fan following as well. This is mostly because of the Evil Is Sexy trope and she's shown to be very competent during her investigation on earth. Lubic gets his share of this as well as he was the only Earth-based character to hold his own against Skeletor's forces.
Foe Yay: One of the first things Skeletor states in the film is his desire to have He-Man kneeling at his feet and after arriving on Earth he spares the other protagonist's on the condition He-Man becomes his slave. However none of that holds a candle to his reaction to having He-Man whipped.
Frank Langella's take on Skeletor is one of the most triumphant examples of this. He's on record saying that it was one of his most favorite parts he's ever played, and he was clearly having a ball.
Dolph Lundgren, meanwhile, doesn't have any particularly interesting lines, but he's bare-chested and muscular and swinging that sword around as often as possible; and hey, they weren't paying him to talk!
Also, Christina Pickles and Courtney Cox would reappear together in Friends years later, with Pickles playing Cox's mother (though in comparison to how the Sorceress healed Julie's injuries here, Judy and Monica Geller's relationship isn't that great).
Similarly, Dolph Lundgren's career recently had a bit of a revival with the Norton Antivirus commercials and his appearance in The Expendables. Those too young to remember his Rocky IV performance may have this reaction.
Rooting for the Empire: The heroes are somewhat bland with some cool and funny moments here and there. The villains consists of the entertainingly over-the-top Skeletor, his attractive and competent dragoness Evil-Lyn, the Carnival of Killers and Darth Vader-esque mooks. There's little question on who steals the show.
So Okay, It's Average: The movie isn't good by any means, with large deviances from the source material, too blatantly mimicking Star Wars and the trip to Earth never really fits the tone of the franchise. But the overall product shows signs of effort, with some fun action scenes and a few memorable performances, resulting in a film that's somewhat watchable.
They Wasted a Perfectly Good Plot: Instead of the Earth subplot and its residents, a movie that involves He-Man leading a group of resistance fighters to overthrow Skeletor's reign would've been a better movie.