Our main character, Twilight, and her faithful companion/assistant/surrogate brother Spike is set out on a quest to make friends against her will, instead of averting a disaster... or so she thinks. Hilarity ensues as she tries to avert the disaster instead. Also, this gives us our first look at the other main characters as she gets to interact with each of them.
The execution of this plot is pretty solid all around, the scenarios flow well into eachother and everything makes sense. The writers made sure to have an organic way to set up the entire scenario. While cartoon logic dictates that we will see the disaster unfold, Celestia's odd answer works because from what we've seen, it's clear that Twilight really does have problem with socializing, and that it could cause her trouble. By giving Twilight a actual task, she is forced to actually meet other people and interact. Then we end up with a suspenseful cliffhanger.
The comedy in this episode is great. The comedic timing is spot on, and the dialogue is fantastically funny almost throughout.
However, the one part of the episode I have to complain about is actually the characters. Outside of Twilight and Spike, most of them are very one-note. AJ is a friendly but loud family person, RD is a lazy but justifiably cocky jock, Rarity is simply a fashionista who wants to go to a classier town, Pinkie Pie is an over the top silly party animal and Fluttershy is just... very shy.
This is actually a pretty glaring issue since this episode should be setting up the characters personalities, but they are pretty much just cardboard cut-outs for now. Still, a very solid starting episode.
As for the backstory...
Jealous sibling went bad and wants revenge. It's a very overused scenario, but for good reason, and I can't fault the backstory because it is very concise and solid.
Now on to the sadly much weaker half of this two-parter...
Now we get our main cast together on a quest, and they are off to find the Elements of Harmony, our dear MacGuffin. However, they must all face a series of trials by Nightmare Moon to reach them, and then defeat the nefarious villain.
The episode starts falling apart on itself pretty early on, sadly. Why is Nightmare Moon even giving them trials, and not attacking them outright? Later villains have excuses for why they didn't go this route, but NMM doesn't.
The trials themselves are hit-and-miss.
Fluttershy's is one of the better ones, even making reference to a greek/roman myth(a pegasus doing that? Neat.), that of Androcles and the Lion.
On the other hand, we have AJ's trial which doesn't at all reflect her element at all. Perhaps we should've had trust instead of honesty? Wouldn't help that much- the scene is still forced and out of place(and makes AJ look like an idiot).
Rarity's is solid in regards to her element, but breaks the mood of the episode, being quite a bit silly. RD's fails to have any stakes, because there's really no reason for her to join the Shadowbolts whatsoever. It should've been illusory Wonderbolts. Pinkie's trial is pretty well done, though.
The conclusion is good enough, bringing the pilot to a satisfactory end.
Part 2 on it's own is one of the weaker episodes in the series, to be honest. However, as a whole, Friendship is Magic is a pretty good pilot(mostly due to the strong first episode). It has a lot of problems, but most pilots do, since the writers haven't quite learned to play to their strengths yet.