It was a beautiful day in Canterlot. Three friends named Zephyr Dash, Crystal Dancer, and Dream Treasure were playing. Zephyr Dash was a Colt, while Crystal and Dream were fillies. "Hey Zeph and Crystal, watch this!" yelled Dream Treasure. Dream Treasure zoomed down an electricity wire on a skateboard. "WHOAA!" screamed Dream. CRASH! Dream Treasure hit the ground. "Dream! Are you okay?" said Zephyr Dash. Crystal Dancer sighed. Another attempt to get they're cutie marks, and it failed. Zephyr Dash already had his Cutie Mark. It was a Wrench and Screwdriver. It represented his ability to fix electronics. He could fix anything, as long as he had at least 30 minutes to do it. He once fixed a computer that was completely smashed in 5 minutes. He was the most skilled Engineer that Canterlot had ever seen. "Hey, what's that?" asked Crystal Dancer. "EVERYPONY RUN!!!" yelled the Chief Police Pony. Screams of fear were heard as a tornado ripped threw East Canterlot. It didn't do any damage to the town they were in, though, it just sucked up Ponies. "It's a X-33.5 tornado! It's known to suck up ponies and steal they're cutie marks! It's supposed to come around every 500 years! Anypony who gets sucked up needs to re-earn they're cutie marks! We better run!" explained a frightened Zephyr Dash. All of a sudden everything went black. The three friends could not see or hear...
THE NEXT DAY...
Zephyr, Crystal, and Dream woke up in the West Canterlot hospital. "Ughhh... what happened?" moaned a dazed Crystal Dancer. Suddenly Zephyr remembered something! "OH NO! I gotta check to see if my Cutie Mark is still there!" Zephyr Dash quickly checked his flank, and to his surprise, his cutie mark was still there. "What? How is my Cutie Mark still there?"
"You three weren't sucked up by the tornado, but you were all temporarily deafened and blinded. Rocks just hit you in the heads, thats all. Three guards came by and got you. Your lucky you weren't sucked up, ecspecially you, little Engineer. Right now you are in the West Canterlot Hospital." explained the nurse. "Oh and one more thing, you all have a couple of guests. The nurse left the room and to Zephyr, Crystal and Dream's surprise, Princess Celestia and Princess Luna walked in...
SORRY EVERYONE! Chapter 2 will be up soon. I need to get some ideas! Thanks for reading chapter 1!
This moves waaaaay too fast.
Zephyr Dash, Crystal Dancer, and Dream Treasure? Those names just reek of Mary Sue-ness, but I can't completely evaluate the characters yet because you gave them no time to develop. We know that Zephyr Dash is good with electronics (which don't exist in Equestria, but I'll let that slide). Like I said with names... That has nothing to do with his talent, and I'm guessing you chose a cool-sounding word at random.
Extend the intro scene (and break it up into paragraphs). I can't distinguish between Crystal and Dream, neither of them are given enough time to show individuality.
Suddenly tornado, everyone gets knocked unconscious by... rocks? And then the Princesses are there. Work on your pacing. You should try to go for chapters over 1,000 words each. If you added more detail to just the events in this chapter, you could easily reach that mark.
And other than that, get a proofreader to help you with your grammar. You want your story to be as good as possible before you actually choose to present it. And some stylistic things - look at how you used the phrase "cutie mark is still there" three times in a row. It sounds awkward.