Let's take this from one end to the other. *cracks fingers*
The term of being "truly evil" is something I would interpret when someone hurts other, for the joy of seeing them suffer. They do it regardless of the feeling of their victims and they do it for no other reward that to please oneself. Discord, as you brought up yourself, was someone I would see as "truly evil" for the same reason as the one you posted. He had no greater motive other than to have fun, which is something he achieved by hurting other, maybe not directly but he still brought despair to the lices of many ponies just for his own amusement.
This is what I would call being evil. When you act mean towards one or more individuals with no other goals than the one of your own amusement and joy.
About the feeding system of the changelings, the only reason we interpret eating as being something physical is because that's the way we convert different materials to energy and resources in out body. My bet would be that the changelings use the consumed magic/love as an energy resource from which they use the energy as we would use the energy of the food we have consumed. I think, as she said that they needed to feed, that this was her intentions and the reason she wanted to "take over" Equestria was to preserve their source of "food". I don't think they ever had any intentions of hurting the ponies, but that they simply used the only method they knew to acquire this magical energy.
About my theory of Chrysalis wanting more is because of my interpretations of the song "This Day Aria" simply because I hear her singing not only against the real cadence, but also making double standards against herself. It often sounds like she's trying to disprove herself on the matter of wanting love for the love rather than the energy.
I believe the reason she was "enjoying" doing this may have been for several reason. She might have grown power hungry after defeating Celestia, as any other would in a ruse of ecstacy, they would enjoy it. It could also be from the fact that her plan of survival were working out very well, she saw how her species were acquiring this much needed magic of love for their survival.
I don't think every story needs an antogonist, and calling the rest of the Mane 6 antagonists in episodes such as Lesson Zero is a bit much in my own opinion. Twilight was troubled, she was definitely the pony in focus, the protagonist without doubt, but she was not up against the rest of the Mane 6, they were not the evil ponies in this episode. If we HAD to name an antagonist of this episode, I believe it would be Twilight herself, because she's the one getting herself overworked on this, she's the one trying aimlessly to find a shortcut by creating a problem, hence being the "bad pony".
In the episode of Iron Will, I believe Fluttershy was the Protagonist and with the help of the semi-antagonist Iron Will, he created the bridge for Fluttershy to become the real antagonist of the story. The protagonist seeks help, but instead of getting the help she needed she's turned in the wrong direction and thereby becoming the antagonist against her own will. This is why Iron Will should be considered the true antagonist on this episode because he was the cause of Fluttershy's change.
I know right? It's wonderful to see the complexity at work, but think of this: They're more than one writer and when people can discuss various ideas for episodes then it will always create more ideas, new and more intriguing ideas as they bounce these ideas between eachother. It's easily learned, just find something you do, then find someone who does the same, then do this, together.
I wrote a pony poem with Neikos once, where we wrote one line each. When we had set the first 3 lines we had the story, together.
After that it simply flowed, we knew exactly where we were going without barely trying to come up with an idea.