This title might make you think this is my complaints about the villains. Actually, it addresses the complaints of others about the villains.
What a lot of people complain about is that villains only last two episodes. Nightmare Moon is rendered effectively dead when the Mane 6 use the Elements of Harmony to destroy the darkness that possessed Luna and restore her to her true form. Chrysalis's fate is unconfirmed (unless you go by comics as canon) but she's most likely dead unless she has Team Rocket immunity or is faster than Rainbow Dash (and some are inclined to think either since they love her too much to want her to be dead (see other blog for details). And King Sombra? His death should have been clear, but people still debated it until Meghan McCarthy confirmed it.
Discord on the other hoof (who is fan favorite villain) returned, but his return episode was about reforming him rather than defeating him and he's not evil anymore. Sombra's death and Discord's redemption will be addressed later, but right now I'm at the "appear in two episodes" thing.
What some people don't seem to realize is, My Little Pony: Friendship is Magic may not be the little girl show Hasbro initially intended it to be, but it isn't Dragonball Z, where main villains can last as long as 59 episodes (the record set by Frieza, plus he returns 13 episodes later and dies three episodes after that). It isn't Sailor Moon or 24, divided into seasons with individual threats and villains all the way through who aren't defeated until the end of the season. It isn't Supernatural, which keeps the villain Crowley (though initially shown as a protagonist) around for four seasons because we love him and don't want him killed. It isn't even Digimon, which has arcs revolving around fights with main villains. (Ep 1-3: Wild MotW's. Ep 4-13: Devimon. Ep 14: Get the crests. Ep 15-20: Etemon. Ep 21: Kari's introduction. Ep 22-39: Myotismon. Ep 40-52: Dark Masters. Ep 53-54: Apocalymon. Season 2 divided into three ending with resurrection and final death of Myotismon as main villain.) Antagonists in Black Lagoon don't last much longer than two episodes anyway, with an average of three. And it's certainly not Pokemon, which keeps villains around for infinity episodes and doesn't bother defeating them for good (with the exception of Hunter J and Cyrus, who both die at the end of their season, and most of Cyrus's minions arrested).
Point is, My Little Pony: Friendship is Magic isn't all about fighting some main villain. It's about the ponies, their life in Ponyville, Twilight learning about friendship, character development for the ponies, and other minor adventures with entertaining storylines that don't have to have a villain, beyond the occasional bully (like Diamond Tiara, Silver Spoon, Gilda, and Babs Seed), jerk (like Trixie, Flim, Flam, and the teenage dragons), or monster (like the Hydra, Timberwolves, Windigos, and the cannibalistic dragon). Sure, Diamond Dogs are a little more sinister, not to mention Trixie in her second episode, but the show doesn't need to have villains to be entertaining, though I admit the episodes with the villains are among my favorites. But part of what the show is, kind of a unique tradition for the show, is that main villains like Nightmare Moon, Discord, Chrysalis, and Sombra appear in two-parters that begin or end a series. And really, they don't need to appear in more. A return outside of the comics could be a little repetitive unless there's a pairup, and they can make room for new villains by disposing of the ones they have and satisfying those who don't like karma houdini by giving them an official defeat. Kinda like the Bond villains after Blofeld, not one MAIN villain survives past a single movie starting from Live and Let Die. It did exceed my expectations bringing Discord back in an episode in the middle of a season, but like I said, he was less of a threat in that episode and the main thing was reforming him.
So, that wraps up my "two-episode" thing. Now comes the complaints about the permanent end of the evil of two villains. Somehow nopony complained about Nightmare Moon even though she's either reformed (assuming she's Luna corrupted) or dead (assuming she's a manifestation of Luna's jealousy possessing her), and people believe, or atleast pretend to believe, that Chrysalis will make a comeback or atleast is just banished. (and that's just the ones who think of comics as non-canon, the ones who look at them as canon can have satisfaction in that she gets a whole four-issue comic with her as the main villain, and again, survived but imprisoned).
King Sombra is dead. The Crystal Heart vaporized him, and more graphically than Tirek or Lavan. Chrysalis didn't disintegrate and we never found the body so her fate is up to us to speculate for the time being. Sombra is clearly dead, and WordOfGod confirmed it. Though some (like me) were satisfied 100% that there was an actual death in the show and it was spectacularly done to the most evil villain, others complain that we can't see more of him, he can't make a comeback, get more lines, have his backstory explained. Some on account of "killed off too soon". Some even think the writers gave up on him. Well, that we don't know much about him makes him more mysterious. They always could do a backstory episode or even movie revolving around Celestia and Luna fighting Discord and Sombra in the past, but if it explained much about Sombra, people would probably complain that it makes him less mysterious, I know some complained about Star Wars Episodes 1-3 revealing more about Palpatine and making him less mysterious than Return of the Jedi portrayed him. (His name was never even mentioned in RotJ, they just called him "Emperor") And they had to kill atleast one villain, remembering what happens to Tirek in G1, which is all right but inferior to G4. I already addressed the "return" thing above, and in any event many feel he is the worst villain and has less return value than Discord or Chrysalis. (I personally have him my second, below Chrysalis and above Discord, no offense to Discord and I still like him)
Speaking of Discord, it's time to get to him now. Our Spirit of Disharmony was reformed by Fluttershy and will use his power for good (most of the time). Before the episode even came out, people said it was not possible for him to turn good. Now many complain that turning good ruins his character, he's not the evil Discord we knew and loved. Well, we still have two episodes of him performing chaos, kinda three, and as I said above, it exceeded expextations just to have him return in a later episode. And now that he's good instead of encased in stone, we can expect him in later episodes, maybe some cameo appearances performing harmless pranks alongside Pinkie Pie and Rainbow Dash. Maybe even a fight scene between him and a villain.
So... I hope the same people who complained about Sombra's death aren't among those who complained about Discord turning good. What if Discord, the fan-favorite villain, had died, and Sombra, the most evil villain, had turned good? Ensure the fan-favorite villain doesn't return in later episodes, and "ruin" the character of the villain known for being pure evil and a dark presence. Honestly, between the two, if you had to choose one to turn good and one to be killed off, which would it be? I'd go with what happened in the show.
And I think if Chrysalis returns, whether she dies or turns good will surely generate complaints from the ones who complained about the former with Sombra and the latter with Discord. I think it's better off to leave her off at her fall and let us make up our own minds. Basically, each person has their own preferences, their own opinions, their own likes and dislikes, so it doesn't matter what they do, they can't please everypony. Otherwise they might end up pleasing nopony.