There are pretty high odds that at least one of the Mane 3 pony pegasi are Changlings. Rainbow Dash, Fluttershy, or Scootaloo.

Actually, it would be kind of funny if NONE of the pegasi were normal pegasi, and were all hybrids of some sort XD

They've given quite a bit of evidence to each.

Fluttershy? Dragonshy (Pony-Dragon Hybrid/Dovakin): Hard to say if she has a family being a hermit, (I personally imagine she has a lot of overbearing athletic older brothers) but it would be interesting if her fear of dragons and not all other forms of beasts is due to projection of her own fear of herself and her father, and her repressed side of her personality is due to her dragon genes (yes this is partially inspired by Witchcraft is Magic, but its a funny, clever theory anyway)

Scootaloo? Changeling: (One of the few changelings that escaped the hive life, like Bon-bon is suspected of being) This gets into the more serious of theories. She's just a child but wants a big sister so she doesn't have any evidence of family ties. Before sleepless in ponyville, the 'looking for adoptive big sister Rainbow Dash' Scootaloo was just Fanon, then suddenly became Canon. As proven by steroid pony, the size of wings does not effect the ability to fly, but the same might not be true for changelings. Scootaloo is constantly around her loving friends so she stays well, but she never takes any love so her physical development is detrimented and CAN'T FLY. When she does try to fly, she very often BUZZES HER 'FEATHER' WINGS AROUND LIKE A BUG.

Rainbow Dash? Demi-goddess (Heir of Equestria and lost daughter of Celestia herself): This gets into one of the longest set-ups in MLP history. She's not a hermit and has been to many Pegasi events where she participates yet shows no signs of parents. Has the same rainbow energy as the elements of harmony coursing through her very movement. Created a Sonic Rainboom at an unbelievably young age that formed the NEW Elements of Harmony, of which Celestia was the last heir of its OLD power but lost her connection to it sometime after Luna's banishment, possible inheritance. Has Rainbow hair almost like the Princess, and both are light-based ponies; one sunlight, and one sunlight through a spectrum. Has the cutie mark of a Greek demigod, and always wears Greek clothing to match it, both in armor and in dresses, possible huge hint to all those who have seen Hercules. A Sonic Rainboom appeared when the Elements were released to stop Discord, establishing her connection to the elements as not just a coincidence in Rainbow color. In sleepless in Ponyville, it confirmed her childhood of getting over her own fears weren't ones of comfort, but desperately getting stronger then anything she feared, meaning she practically raised herself. Showed 4 signs of severe monophobia to prove that in show, chronic fear of being alone (Of course, would be incredibly mind-blowing if she was a changeling, and the reason she was so ungodly powerful is because everyone admires her)

i know it's you Chrysalis.so come out and fight me.i have never lost a battle.and armed with my keyblades.(2 fatal crests one original color. and the other white color combined in to one(like a double light saber. but with keyblades)but can be taken off)so do you dare face me Chrysalis?

"They get to experience being with their loved ones, the love they give let us live another day. Fair deal if you ask me."

"NO!!!"

A roar behind the Changeling snapped Rainbow Dash out of the feeding trance. Before anypony could respond, a Unicorn leaped out of the bushes from which she was hiding and fell upon the Changeling, growling, hissing and snarling, screaming bloody murder.

Rainbow Dash watched with shock as the REAL Twilight Sparkle, whom she had assumed to be dead, brought Tartarus upon the Changeling. Each pound of her hooves shattered the carapace and made green ichor bleed from the cracks. With savagery that should not exist in a pony she ripped the horn and the wings of the Changeling right out of their sockets, flailing vessels and nerves trailing behind. She brought her unicorn horn down upon the Changeling at its abdomen, where she ran her horn through and proceeds to gore it. The Changeling was lifted into the air with a burst of telekinesis, where then Twilight's horn glowed and melted its compound eyes with a blast of arcane energy.

At last, bleeding, battered, disemboweled, liquified and bubbling humour trailing down its ruined face, the Changeling screeched one last cry of pain and horror before Twilight threw it with all her telekinetic might against a cliff.

Rainbow Dash winced as the Changeling died with a sickening CRUNCH, which settled into a putrid, messy green smear of gore and chitin upon the rock face. She stood stock still with terrified horror at the sight. Were she not a pony she would lost control of her stomach and hurled with nauseating disgust at the spectacle half-way through.

She turned away to focus at the panting unicorn. She couldn't believe her eyes when she first emerged, and she still couldn't believe it either. Could this really be Twilight Sparkle?

"Twilight? Is it really you?"

The unicorn turned her head to Rainbow. What RD saw made her take a step back in fear - She looked starved and dishevelled. Her mane and coat was unkempt. She was covered in filth, grime and some kind of Changeling fluid. Mixed with it was a body laced with brutal, infected scars, bruises and half-healed lacerations that stretched over her body. Her hoof was bleeding, both from destroying the Changeling moments before, and from what Rainbow thinks look like she had been clawing out of a cocoon and spending days running non-stop.

It was nothing compared to the expression on her face - it twisted into a look of anger, mixed with pain. Her eyes, HER EYES - they were filled with gnawling, all consuming Hate. Rainbow also saw something else; Twilight glared at her, glared through her like she was a spectre. The unicorn was staring blankly into oblivion, as if something happened to her that had scarred her memories, traumatized her, and that sent chills down Rainbow's spine more than the mask of hate.

At the sight of Rainbow Dash, Twilight calmed down, taking deep breaths. "Yes, Rainbow, it's me... It's really me... That Changeling had you fooled, didn't it? Thank Celestia I made it back in time. The last thing I want besides this... is to lose any of you..."

"W-what happened to you? You were gone for a month! Everyone from your brother and the Guards to the Princesses were looking for you! I thought you were dead!" Rainbow Dash suddenly shouted, both from joy at her friend's return and from fear of what she did, "All we found were you bag of notes in the Everfree Forest! What did the Changelings' did to you?"

"Y-you... I... You don't want to know..." Twilight said weakly, now that her adrenaline from her killing the Changeling had gone from her veins and the last few days of exhaustion and agony catch up with her, "You don't ever want to know what they did to me..."

Rainbow Dash rushed forward to catch Twilight as she slumped to the ground with a grunt of pain. "Just hold on! I'll get you back to Ponyville in a jiffy!"

"Yeah, let's do that..." Twilight merely muttered. Then, suddenly, her voice grew cold, and dark, "... first thing I get back... i'll need Spike to get a letter to my brother... and the Princess... they need to know what they did to me... and what we must to do to them in return..."

Rainbow Dash took flight as Twilight slipped into unconsciousness, leaving behind the dead Changeling upon the cliff, like a foreboding statement of the terrible events to come...