Since her diplomatic success with the Yaks, Twilight had hoped that Celestia would include her in more diplomacy.
Doesn't read well with this repetition. Employ broader vocabulary and tweak the flow of the sentence.
As the princess of friendship, that kind of thing really should be up her alley, even if it meant she'd have to leave Ponyville sometimes.
Shifting tense for no apparent reason, comes across sloppy. Pay greater attention to basic details.
cutie map
Might just be my lack of familiarity with the source material, but I have no idea what this is or what it does even with the extra information which follows. What is it, why is it, why does the protagonist have it, why isn't it capitalised like a proper noun? etc.
Celestia sat on her throne, awaiting the arrival of Twilight and the Griffin representatives.
We already know this. Explaining the situation is a good thing, redundancy is, in most cases, not.
Celestia smiled [...] Luna sighed, her face full of sadness [...] Celestia frowned [...]
(and many more instances throughout)
You don't need to tell the reader what a character is doing with their face every time they speak, dialogue often only needs to be slightly more than perfunctory to indicate the psychology behind it.
Luna's right front hoof tapped on the floor as she became lost in thought for a moment, the beautiful stars of her mane swirling even more quickly as her alicorn magic caused it to wave as if with an unseen wind.
The imagery here is stronger than in the prose prior, and doesn't go so far into the purple as to come across parodic, yet it is rather clunkily expressed and it also compares things to things the reader was not already aware of, such as the swirling of Luna's stars ─ it being faster than it previously was doesn't convey the image effectively, since the reader didn't know how fast it was in the first place. Take time to discuss things and give details in your prose, cutting corners just leads to an unsatisfactory reading experience, if not confusion.
Just then, the guards at the door parted way and a stressed looking Twilight ran in, her hooves tapping across the floor at a frantic pace.
What is Twilight feeling as she runs through the door? Give the reader psychological insight into the protagonist, not just superficialities. Furthermore, the reader already knows that hooves make a tapping sound on the floor, communicate something new, perhaps about how the sound carries through the environment or something like that.
Aguila was a female griffin with a white head, deep blue highlights around her eyes, and a light tan that appeared gold on her wings and body. She was larger than her companion Leon, a male with a gray head, darker gray feathers around his eyes, and a dark brown body and wings.
Although these descriptions are very uniform and business-like, it's nice to actually have some upfront information about these characters as we are introduced to them. That said, it would be nice to have a little more characterisation up front. How do they carry themselves, are they interested in their surroundings or merely focused on their reasons for being there, what does that say about their personalities? etc. Again, a little extra detail enriches the reading experience.
I'm fairly done at this point because I'm not very engaged by the story, but it seems from a cursory glance ahead that you repeat the same mistakes throughout, so this should be fairly relevant critique in general. Good luck with your project.