Yes, it will have a happy ending. Honestly I hate many stories that have really depressing endings. The fandom's ideas about the chrysalis Celestia was trapped in, as well as this fanfic called Smoke and Mirrors. I haven't finished the fic, but it also talked about the transforming abilities of Changeling chrisali. This stuff inspired me to have Celestia turn into a changeling, but everything else in this story I basically thought up myself.
This is why I HATE the Changelings so much - the sheer implications of what horrors they would accomplish if they ever win. Because of what they had done to our favorite characters, and what they would do.
Like her all you want, I'm going to hate Chrysalis as much as I hate Discord for mind-raping the Mane Six. And I have to disagree partially with the show on the subject of hatred - when it comes to things like this, it is never a sin to hate what is evil.
Chrysalis must DIE slowly for everything that is happening in this story. And she WILL die.
I don't like Chrysalis either, well, her personality anyway. I really love her design, though. And yes, the implications of the Changelings taking over is NOT good for Equestria. At. All. Honestly, if thought about a bit deeper, the villains in this show are doing pretty awful things to the characters. By making the night last forever, Nightmare Moon will slowly kill off every living creature. Without sunlight, no food can be grown. Discord caused extreme mental stress to everyone in Ponyville with his chaos. Chrysalis and her changelings replaced ponies and fed off of their emotions. Sombra ENSLAVED an entire empire, and filled their hearts with fear.
Yea, when you think in depth about these villains, they really don't seem to likable anymore...
Long story short, yes, ALL of them are unlikeable. And yet the fandom finds them cool and tries their best to redeem them, or at least give them all a complex freudian excuse... But the only good authors I know who could pull something like this was Alex, as mentioned, or Kendell2 (Who wrote a redeem-Trixie fanfic that had since became alternate continuity), or Cryssy- miu with her "Broken Spirit", or ItsfromPeople with his ChaosVerse saga. Otherwise, all just fall flat as merely worshipping Dracos-in-Leather-Pants, or Rooting-for-the-Empire, if you catch my drift.
And they had a gall to give Ron-the-Death-Eater treatments to Princess Celestia!
By the way, the source of my severe dislike of Chrysalis and Changelings in general was due to a pony video on youtube, one of the earliest made to portray the scenario that you're currently doing, only significantly creepier: [link]
Inspired me to write an omake revenge-fic of sorts. Check it out on my account.
Discord causing mental stress? Try out-right mind-raping and psychological/physical torture.
I recommend you read Alex Warlorn's Pony POV series if you want to find all the good reasons to hate him.
Sombra is more of a supernatural, Sauron-like presence then a physical villain for much of his appearence, further reflected by his lack of speech. The problem is that the producers did not give him too much characterization in the background expositions, which WOULD make this kind of character work like Sauron from Lord of the Rings, but well, it wasn't enough.
They did it right with the Windigoes though.
Nightmare Moon got wonderful characterizations by her arrogant, bombastic and intimidating presence during her two episodes. And the bronies loved Chrysalis for being sinisterly cool-looking, extremely genre-savvy and being able to pull off that elaborate scheme of hers that came closest to winning as Discord was.
I personally really like "what if" stories. And if you don't like it and don't plan on reading it, why do you feel the need to make a post on how you hate the villains and stories like this?
Also, technically we don't know what the Changelings would have done, it would have obviously been bad, but this is all just part of a fan story where nothing is canon. So wishing for anyone even the villain to die seems a bit too much.
Personally I really like dat transformation going on.. aaaaw yea... God, I think Deviant Art is getting to me. Before you know it I'll be drawing bloated sonic OCs and posting even the most personal parts of my life on here.