I just finished the first part though I bet it could use some fixing. Just wanted to see what you guys thought! Here it is!
*It's another beautiful sunny day in Ponyville. The Wonderbolts rocket past in the sky. The scene goes down into the forest and focuses on Fluttershy.*
She walks by and comes across a little bunny rabbit. Remembering that it was one of the new little ones that came two weeks ago and had been avoiding her since the first time theymeet.
“Hi little bunny rabbit” she says softly, rubbing its head with her hoof
The bunny twitched his nose and seemed to calm down for a second then it looked up at her and ran away. She chases after it but it hops into the bushes and dissapears. “Oh well I guess I’ll come back tomorrow and see if she’s here.” She sighs.
As she was walking home Rainbow Dash suddenly flys and crashes into her.
“Ah jeez sorry flutter shy I didn’t see you there. I wasn’t watching where I was flying.” Says Rainbow Dash flapping the dust of her wings.
“Oh it’s alright Rainbow Dash. I’m fine.”
Rainbow Dash looks closely at Flutter Shy.
“You don’t look too happy.”
“Well I…”
“No no no don’t make up any excuses just come with me.” Rainbow Dash says flapping into the air.
“Where are we going?” says Flutter Shy extending her wings and flying to Rainbow Dash.
“To my house.” She says and then flys off with Flutter Shy following.

2303520 If you don't mind, I'll just focus on the negative, because I believe one can grow the most from negative comments (actually I just suck at giving opinions but don't have a heart to leave this thread unanswered).

*It's another beautiful sunny day in Ponyville.

People hate weather beginnings because most of them aren't done right. Many people would stop reading after that first sentence.

The Wonderbolts rocket past in the sky.

Wonderbolts have rockets?

The scene goes down into the forest and focuses on Fluttershy.*

I'm so confused right now. What scene? Am I watching a television or something?

She walks by and comes across a little bunny rabbit.

Usually when you first introduce a character you start with more than just a 'she'

Remembering that it was one of the new little ones that came two weeks ago and had been avoiding her since the first time they meet.

Good.

“Hi little bunny rabbit” she says softly, rubbing its head with her hoof

Good.

The bunny twitched his nose and seemed to calm down for a second then it looked up at her and ran away. She chases after it but it hops into the bushes and disappears. “Oh well I guess I’ll come back tomorrow and see if she’s here.” She sighs.

Good except for mixing past with present tense. People usually use past tense to tell the story. You can do it in present tense, but stick to it if you do.

As she was walking home Rainbow Dash suddenly flies and crashes into her.

flies -> flies in
I'd also include something about his new maneuver or something. Rainbow Dash is supposed to be a good flyer. Just crashing in would work for Derpy, but Dash needs a bit of explaining.

“Ah jeez sorry flutter shy I didn’t see you there. I wasn’t watching where I was flying.” Says Rainbow Dash flapping the dust of her wings.

Why wasn't he looking? Because there was obviously something more important to her. What was it? We readers want to know about important things. Tell us she was watching Wonderbolts as she was flying or something. Also, Fluttershy might have broken something and Rainbow Dash doesn't even care. All she cares about is dust on her wings? She is full of herself, but not at the expense of her friends.

“Oh it’s alright Rainbow Dash. I’m fine.”

This would make more sense if Rainbow actually asked if she was fine.

Rainbow Dash looks closely at Flutter Shy. “You don’t look too happy.”

Who looks happy after getting hit by a pony?
You could do something like: "I'm just fine..." said Fluttershy, lowering her head.
Then Rainbow Dash's question would make more sense.

“Well I…”

“No no no don’t make up any excuses just come with me.” Rainbow Dash says flapping into the air.

Excuse for what? Dash didn't even invite her to anything. She was asking Fluttershy a question and she didn't even let Fluttershy finish. This doesn't make a lot of sense to me.

“Where are we going?” says Flutter Shy extending her wings and flying to Rainbow Dash.

She's very obedient apparently. I'd have her fly after getting an answer to where they are going. Let's not forget how another Dash's invite went down in a past (invitation to watch dragons migrate). Not sure if Fluttershy is that trustful toward Dash.

“To my house.” She says and then flies off with Flutter Shy following.

If you're writing a clopfic, then I guess this sentence is acceptable. But if you are writing something more then I think you should explain more. I would think that Fluttershy would ask more. She wouldn't just fly for few minutes without knowing what Dash has in store for her.

I think your writing is good. There is a lot of action and no useless scene descriptions that even good authors usually overdo (that's just my personal preference though). The story is driven, things are happening, but things are to confusing because they just happen without much explanation. If you could explain some things a bit more then readers could follow your story easier. As it is you leave the reader in the dark and that usually just confuses readers.

Keep at it and try to get as many opinions as possible. That's the best way for bettering a story.

PS. I hope I did more good than bad by replying.

Thanks for your response Dragor I really appreciate your critique. By rocket past I meant like they were going really fast. I'll make some changes and write more of the story. Love~Derpy L