Are the comics canon or Alternate Continuity? I've seen it argued in both directions. Yes, they're officially licensed, but that doesn't necessarily make them the same continuity.
The comics follow the shows continuity but the show does not.
MLP:Fi M # 1 - # 4
What are "infected" ponies and how does Twilight know about them? I first assumed that they were ponies under a spell, like Cadance's bridemaids and Shining Armor in A Canterlot Wedding, but the dialogue and all the captured ponies suggest they are changelings in disguise. However, the changelings impersonating Derpy and Pinkie had neither permanent glowing eyes nor a zombie-like behavior.
From a Line To God: They aren't really zombies... just not really putting any effort into the charade of taking over Ponyville. They don't really need to since the whole thing is just a first step in Chrysalis' plan to lure the Six to her.
It seems pretty clear the changelings "infected" the ponies like Chrysalis did to Shining Armor and her bridemaids, then brought them all to the town hall and started cocooning them so they could take their place.
How does Fluttershy know the queen's name?
Just because it isn't mentioned in A Canterlot Wedding doesn't mean no one knows it. Presumably Celestia would at least know the name of the ruler of a kingdom just south of her own.
Or, quite darkly, this is one of many different 'Changeling Kingdoms' created in Chrysalis and her army's conquests. It's quite possible they have a homeland somewhere, but have obtained many different kingdoms/colonies over time.
In the Italian dub — and possibly other foreign dubs, I haven’t checked — Celestia does call her Queen Chrysalis. (Because her name was in the script, after all.)
Why do the Mane Six fall so easily for the Changelings' ruse to break their friendship? It's not like they're unaware that they're going up against shapeshifters who thrive in sowing exactly this kind of discord amongst ponies. You'd think Twilight at least (the one who first caught Chrysalis' bullshit last time) would have suspected something was off.
MLP:Fi M # 5 - # 8
So, why exactly is Rarity, not Twilight taken by the horrors? Rarity seems to be much stronger willed and harder to snap, after all, not to mention much less combat capable. Also, why exactly Mane 5 + Luna took Spike with themselves? Yes, out-of-story answer is probably extra-clichéy repetition of ending of Secret of My Excess, but how characters justify that in-story? They never take him to fight villains in animated series precisely because he is a load and would just be 'dragon in distress' next to any serious villain, which these undoubtedly are. Why Celestia and Luna didn't call Mane 5 on this?
While I don't know about Rarity (it could just be a target of opportunity), but Spike has the ability to send messages and objects between himself and Celestia. That could probably be very useful.
The problem with this is, pony they had greatest need to contact, expert on nightmares, Luna, was right there with them. Doesn't Luna/Twilight team have any other way to contact Celestia? I find it hard to believe.
It seems perfectly logical to me. When it comes down to it, what trait did the Nightmares exploit in Luna? Vanity. She wanted people to appreciate her work. Rarity is the most compatible with that same flaw, and the easiest to manipulate because of it. The others, not so much. As for Spike, they wouldn't be likely to stop him with Rarity involved. He helped with the Diamond Dogs, after all.
Ha, called it.
It looked like they exploited her generosity. Which is fine and well, but Twilight can be exploited even easier, and seems to be much more powerful combatant. Sparkle, shown the same tempting image as Rarity (friends abandoning her) would fall twice as fast and as hard as Rarity - remember what happened when she thought she would fail to write a report?
They didn't exploit her generosity at all. You're missing the point of her nightmare. Rarity's issue was rejection. She was afraid that what she did would not be appreciated. Same with Luna. Her beautiful night was rejected by sleepy ponies. This wouldn't work on Twilight, because Twilight's only fear of rejection comes from Celestia. It's too specific to be manipulated reliably. The last time Twilight's friends went crazy, she rolled with it until she failed to do what Celestia asked of her.
Rejection wouldn't work on Twilight? In The Return of Harmony, thought her friends abandoned her causes Twilight to break without Discord's input. In Lesson Zero, it causes her to dive into deep end and lose any inhibitions in using her magic. In Canterlot Wedding, it causes near total breakdown. Compared to Rarity being rejected in Green Isn't Your Color or Sweet and Elite, where it only makes Rarity angry and causes her to work harder, Twilight is exceedingly sensitive to rejection...
In "The Return of Harmony", it wasn't just being rejected by them that broke Twilight, it was that combined with her complete failure to stop Discord that did the job. She pressed on even after pointing out that they had outright become jerks. Only when there seemed to be no hope of fixing things did she finally quit. In "Lesson Zero", your example is pretty much the exact opposite of what Nightmare moon would need. Her friends treating her issue as an overreaction only made her more determined, not less. Finally, in "A Canterlot Wedding", her friends didn't believe her from the start, and it was only a very public humiliation that knocked some apparent sense into her. Even then, Twilight didn't break. She apologized. Twilight's issue isn't rejection, it's failure.
Exactly. Spike might be willing to stay behind normally, but not with Rarity. Trying to convince him otherwise would be a really dick move. And Rarity (along with Rainbow Dash) has always been the one who struggles most with her darker impulses, Twilight on the other hand is rule abiding to the point of madness. Twilight is easy to fool, but I doubt she would be so easy to corrupt.
But Spike was taken only because he was already in place and could dig. What happens in all other episodes? Friendship is Magic, part 2, Dragonshy, The Return of Harmony, The Crystal Empire, every episode Twilight and Rarity go do something dangerous Spike is unceremoniously left at home. Even in Sweet and Elite, episode where Mane 5 took short, safe trip to Spike's pretty much second home for Rarity's birthday he was deemed to young to travel. Why accept him now?
All of those episodes have Rarity going on a dangerous mission. Rarity herself is not in direct danger. Her being in danger is how Spike got himself into the one mission where it was actually an issue, and so to is this one.
I'm guessing they couldn't resist the Actor Allusion. Coming up next, Nightmare Granny Smith!
Don't get your jimmies in a bunch! Word of God says that Rarity has a Dark Secret that's the real reason why she was chosen to be the Nightmare's vessel. Looks like we'll just have to wait until the next issues come out, and hopefully all shall make sense.
Where in the hoof is Applejack's hat? She's never seen with it throughout the entire arc.
MLP:Fi M # 11 - # 12
Fridge Logic: In the Dungeons and Dragons analogue, "elves" and "dwarves" are treated as add-on adjectives, i.e. "dwarf mule" and "elf pony". This is in addition to their classes, i.e. "dwarf mule barbarian". Shouldn't "elf" and "dwarf" be species alongside mules and ponies?
They are. Dwarf mule is simply the species. So is elf pony. I'm sure if there were more than one sentient species in real life Dungeons and Dragons would have multiple "real world" ones combined with "fantasy" races.
MLP:Fi M # 17 - # 20
One of the mane problems this arc has is it's logic. At first, it seems normal: If you're hurt, imprisoned, or killed, your counterpart suffers the same fate. However, it is never explained why Mirror!Sombra is alive while his counterpart was killed.
Doesn't have to. Before Celestia and Star Swirls visits the world were "kind of" parallel.(Kind of because the only parallels we have is that Celestia is Evil, Sombra is good and Luna didn't became Nightmare Moon), after their visits increase, actions in one world start to affect the other in small, but not exact opposite, ways, the biggest one is Luna's alignment. At the start of the saga, Evil!Celestia thrashes Good!Celestia very badly, but doesn't show to be hurt herself, and later the paradox becomes worse, and hurting one hurts the other, which means that that was not the case before, ergo, Sombra being evil in the main dimension didn't affect at all the good Sombra, since it didn't affected his alignment. However, if that is still the case, Discord being reformed isn't very good news for that dimension...
In regards to Discord. It probably doesn't work like that. Since the mirror world Celestia and Luna changed alliances from good to evil, the "normal" Celestia and Luna should have become evil. At the very least, when the dimensions are so close to being one, the only things they share are physical. Probably.