Now, pretty much everything that the villain, Skeletor, did wrong is covered in that big list we've all seen, the one that describes what not to do if you're the bad guy. The minions couldn't hit the broad side of a barn from ten paces away, the villain was overconfident and too flashy, the evil lieutenants were untrustworthy. Plus, I missed the first part, so I don't know how Skeletor took over...erm...from my memories of the cartoon, it must have been Castle Greyskull, since the Sorceress was there. But he somehow managed to do it, and that's pretty good. Oh, sure, it's only guarded by a non-combatant in a frilly outfit, but still, it's the good guys' base, or source of power, or...look, it's important to them, and the bad guy grabbed it right off the bat. That's the kind of can-do spirit you want from your megalomaniacal villains. Lots of points right there, because it confused the good guys. Maybe it even demoralized them, but I'm not sure about that. Nor am I sure why he kept the Sorceress alive, or why he didn't at least put guardrails around the pits on either side of the throne. Who the hell asks for "yawning chasm" feature when designing their dream throne room? It's not like the heroes ever fall into those things. Now, because everyone knows that by the time the hero (or your damnable turncoat lieutenant) finishes you off by tossing you into the pit, the battle is already lost, when I build my center of power, it will have what appear to be bottomless pits (through clever use of mirrors), but which are actually heavily padded chutes leading to my escape craft.
Skeletor also, of course, had minions. A surprising number of them, and they looked decently menacing. Sure, their all-black armor didn't serve any protective purpose, but it never does. They all looked like mini Darth Vaders, and he had enough to send wave after wave of them to keep He-Man and friends busy for a few minutes, which is about all that you can expect from cheap, generic minions. Some of the minions even served as air cover, although they did this by riding really stupid hoverboards. But attacking from the air is a good idea, and one that minions don't exploit often enough.
Skeletor's lieutenant, Evil-Lyn, was certainly untrustworthy, but that's what you get when you hire an evil right hand. But she was at least clever enough to use the endless wave of suicidal minions as a diversion and look for a back door to the heroes' hidey-hole. Sure, clever minions are always potential problems, and you do have to balance the usefulness of original thought with the possibility that they'll realize that they can take a few dozen minions and challenge your power. But I think Skeletor found the key to assuring her loyalty: Make your lieutenant wear an outfit that looks like an ice skating costume, only more humiliating. Who is going to follow a leader who looks like a dork? Unfortunately, Skeletor, drunk with power, forgot this simple rule and (I'm not sure how) transformed his perfectly menacing black robes into a gold "Aztec god" outfit, complete with an overly-horned helmet. So, of course, He-Man then proceeded to kick his skeletal butt. So the lesson to be learned is that an effective evil genius dresses to impress, and not to excess.
Oh, and never bring a staff to a swordfight, even if it is a shiny goat-headed staff.