Idem

On the whole, I think you're over-thinking it. Sometimes, entertainment requires to sacrifice logic for aesthetic. Still, I'll try to answer your concerns.

The first song about how everything is perfect. This is one of the most classic comedy tricks. Singing for no specific reason that "everything is fine" is a clear indicator that, soon, something will go awfully wrong. And we quickly see that, indeed, something is wrong. I honestly don't really see why you noted it at all.

Rarity organizing weather because of her cutie mark, ok that is indeed not coherent. But I'll call show aesthetic on this one: We need the change to have catastrophic consequences, to cause problems for everyone. And I think that messing up the weather can cause much more damage than running and doing stunts. Sure, the stunts can cause damage too, but the weather causes specific damage that I'll come back to later.

Then, AJ with Rarity's cutie mark, I think you are mistaken here. Rarity's personality and talent is not to find gems, it's much deeper than that. The gem finding spell is just a perk of her talent. What really makes Rarity who she is is her ability to see and reveal the beauty hidden everywhere. Finding gems inside of rocks is one application of this talent, creating beautiful dresses out of simple fabric is an other one. No incoherence here.

Where did they wake up? No indication whatsoever, we can imagine whatever we want. I personally think they just woke up in their normal beds thinking "Why the hay didn't I take a house closer to where I work?". I think the ponies had enough on their mind to not pay too much attention to that.

How can Rarity move clouds? Easy : unicorn magic. Each unicorn has specific powers linked to their cutie mark etc. but all of them are able to use a kind of telekinesis, and I don't see any reason for it not to work on clouds. Twilight did once cast a spell allowing her friends to walk on clouds. Rarity is certainly not good enough with magic to do that, but she can at least manipulate the clouds in the sky.

Exactly how did the spell change their destiny, reality etc. is unclear. But honestly, I don't think there is a single way to organize all this so that it all makes sense. As I see it, the spell affected everyone's mind, but only their minds. For example, Rainbow Dash woke up this morning knowing thinking she has to tend to the animals, and the animals woke up expecting to see Rainbow Dash, and for them, it was all normal. However it is the very first time that RD actually does this and things soon go wrong because, obviously, she doesn't know how to do it, since she's never done it before.

Why are Twilight and Spike not affected? The spell is apparently directly aimed at the elements of harmony, but the element of magic was never "equal" to the others, it always had a special status, and here is a consequence of this: the element of magic, the only pony with the skill to cast the spell, is unaffected by it. (Interestingly enough, once the spell is complete, she's the only one affected by it, although each elements is used to "power" the magic).

As for Spike, either his connection to Twilight, or simply the fact that he's a dragon. Obviously, Fluttershy's critters were affected to, as they expected Rainbow Dash. So not being a pony, not having a cutie mark, is not enough to evade the spell. But dragons are powerful creatures with strange powers, so I wouldn't be surprized to see them resist magic. Especially a dragon hatched by magic like Spike

Rainbow about to get eaten by the animals? Come on, that's pure cartoon comedy. Have you never seen Looney Tunes cartoons where characters get shot multiple times, drink a glass of water and have the water spill out by each hole? This is no way more dark/violent than that. It's just funny because it's silly.

No, RD was not able to understand the animals, that's pretty much the problem, and that's pretty much Fluttershy's talent. I don't see what point you're trying to make here.

Rarity is no good with the weather. There probably are a bunch of pegasi who COULD lend a hand, but why WOULD they? They also have jobs to do, and remember, in their minds, Rarity has been doing this job forever, and so far there was no reason to complain since, in reality RD was doing it. Maybe if it continued for a few days, they would organize something, but everything takes place in a single day.

Now, how did Pinkie ruin the farm so badly. First of all, once again I'll call upon show aesthetic. We need the results do be disastrous. if Pinkie was just having a hard time, it would be boring. Also, remember that Rarity is in control of the weather and does a terrible job out of it. That's what I was meaning earlier when I said we needed her to be terrible at weather instead of terrible at stunts. She does such a bad job with those clouds that, with her work and Pinkie's combined, the trees are absolutely ruined in record time.

Concerning the rest of the Apple family, like all the others, in their minds it was perfectly normal for Pinkie to be here, and they thought she had always done a very good job of it. Only this time, it's for real, and at best they are confused as to why she's such a disaster today.

Pinkie getting back to her good old self was indeed a bit too quick. But concerning the other ponies mood, how would you feel if suddenly the person in charge of the weather botched her job, the village's designer ruined the dress you ordered, the animal's caretaker brought your loved pet back to feral-state etc. etc. ? Everything is connected.

Now, concerning the whole alicorn thing, I would say there are A LOT of things that we don't know yet, and that I hope will be explained later. Alicorns have a special relation to magic, that at least is clear. They apparently have access to some kind of alicorn dimension, where Twilight was sent, and where Celestia was waiting for her. Judging by what we've seen in this dimension, it is closely connected to the matters of destiny, and the very fabric of universe, this is absolutely fascinating, and sadly, probably much too deep for a kids show to explore any further :/ I guess we have some fanfictions to write now.

The link between friendship and magic? Have you watched the show so far? It is all about how friendship IS magic.

Rarity's wing where totally different. They weren't pegasus wings, they were butterfly wing, and they were what I'd call a "magical add-on", that can be added with a simple spell, and removed even more easily. Twilight's wing here are a new part of her. And, as has been hinted, there is more to being an alicorn than being a unicorn with wings, especially in terms of magic. Again, I hope we'll learn more on that matter in season 4.

What is Twilight princess of? Dunno. I'm pretty sure we'll know that in season 4. Then again, I don't think being a princess in Equestria has the same meaning as in our world. It looks more like a general status, a mark of how great a pony you are. We'll see how it all goes.

Finally, how can Twilight fly that well? Well, let's get back to Rarity's butterfly wings: She hadn't had them for more than a few hours and yet she was able to do some flying baller. The basics of flying around aren't apparently that hard. Judging by what the wonderbolts do, there are an infinity of hard things to learn about flying, tricks, control, speed, manipulating winds etc. but flying and doing a barrel roll seem quite easy.

"TWILIGHT-SPARKLE’s friends have their CUTIE-MARKS swapped. But there is something wrong with the execution."

The spell didn't swap their talents, instead it swapped their mindset. I imagine that the spell messed with their heads, causing them to believe they were doing what they have always done. They surely woke up in their homes but probably, without much though, they each attempted to go about what they thought was a normal day for them.


"If so, why is TWILIGHT-SPARKLE not affected? Does the spell not affect the one who is casting it?"

"A mark of one's destiny singled out alone, fulfilled." This is what the spell stated. This must be referring to whoever's destiny is about to be fulfilled. Not sure what the spell was originally meant for but this is obviously relating to Twilight here in context.


"Are the animals planning to eat RAINBOW-DASH? That’s a bit dark."

Animals eating Rainbow Dash? I'll let it slide for being comedy.

"So what, RAINBOW-DASH was able to understand the animals."

Rainbow Dash was never able to understand the animals, but that refers back to my first point.

"Isn’t there some Pegasus that can clear the sky?"

Fair point that there should be at least one other pegasus to try and clear the sky, but I'm willing to make up an excuse in my head for that one.

"How did PINKIE-PIE do so badly?
"
Not really sure what to say about Pinkie Pie to be honest. I'll accept the exaggerated effects of her work on the farm (acres of dead trees) as necessary for impact within a 22 minute episode. But yes, a bit of logic is being pushed aside here. At least it wasn't a situation that dragged on that could have been solved much sooner. (Like in the Babs Seed episode. ಠ_ಠ)


"How can understanding friendship help you make new-magic? "

Friendship IS Magic, baby!


"Rarity had wings, so doesn’t that mean that Rarity was a Alicorn in that episode?"

Temporary fragile magic wings is not quite the same as actually becoming an alicorn. I like to imagine that Twilight's biology is actually changed as well as her powers, but we'll surely see more on that in the future.


"TWILIGHT-SPARKLE is now an Alicorn-Princess. The Princess of what?"

*shrugs* Unless you mean to ask if she is in charge of ruling something, then I don't think she's ready to rule yet. She has only become an Alicorn, not a leader. (yet)


"But if that is the case, why is Cadence an Alicorn?"

I don't think I understand this question. We might as well ask why Celestia or Luna are alicorns.


"But how can TWILIGHT-SPARKLE fly that well?"

Uhh... umm... I... don't know.


I hope my take on things has made sense for you and anyone else who reads this.