The Heroverse: The Mane Six

Equestria is not a normal land. Even for a world that thrives on magic, there are a disproportionate number of artifacts and creations that could be classified as ‘paranormal.’ To keep these from falling into the wrong hooves, Princess Celestia commissioned the Watchmen, a group of secret agents dedicated to the appropriation and defense of and from unusual artifacts. Rarity is one such agent.
Her current mission: Tracking down rouge Watchman Twilight Sparkle.
Twilight is on the run after being framed for a crime she didn't commit. In order to clear her name, she has to get to the bottom of one of the oldest conspiracies in Equestria: The disappearance of Nightmare Moon. What exactly do the prophecies declaring her return mean, and how long does she have left?

Twilight has a techno-organic suit that can alter its own shape and manipulate energy to mimic the abilities of other pony races, giving Twilight the abilities of an Alicorn.
Rarity has a magic gun that can use nearly anything she pictures as ammunition, from lightning to chains.

These two aren't super complicated: Warehouse 13 meets the Fugitive.

Applejack is a reporter for the Canterlot Sun. She awoke a few years ago in a hospital with no memory of who she was or what she even is. She looks like a pony sized but, with wings and a horn. However, she can alter her appearance at will, allowing herself to be whomever she wants.
She doesn’t eat food; she devours emotions. She begins to hunt criminals, striking terror in them and leaving them for the police.She doesn’t really care until she begins to date Soarin. Soarin is a beat cop who believes in making a difference. He wants to make a difference, but naturally this gets him into trouble. Applejack uses her powers to save him, in the process revealing her other form to the Mob.
Faced with the fact that the ‘monster’ preying on their men are real, the Mob starts to target them in earnest. Applejack finds herself drawn into a conflict she doesn’t want to be a part of, forced to fight to defend her friends. All the while, she tries to find the answer to the elusive question: Who and what is she?

Applejack has jacked up Changeling powers. She can hover and fly about half as fast as a normal pegasus, and has limited telekinesis. Her biggest strength is her ability to alter perception. She can cast illusions, turn herself invisible, and alter her appearance.

Going for a pulp/noir fiction thing, but I' not sure how successful I was.

There are many worlds. There's ours, where what we can see and touch is real. Where everything is, for better or worse, normal. THen there is the Phantom realm, where thought can become reality. For the most part, these two realms remain separate. But there are places where the two overlap. Places everyone is afraid of, even if they won’t admit it. The Everfree Forest is one such place. In it, there live monsters. But not monsters like we normally think of; these are simply refugees. You see, the Phantom Realm is a miserable place to live, and what few good places that exist are fought over viously. Many fled to the places between our world and theirs for safety, but conflict followed. Not all who came here had the best intentions, and many already here react badly to bipedal tentacles people, no matter how friendly they behave. To protect both groups, it was agreed that there would be an arbiter. The Mage Starswirl forged a Mask of Power, imbued with the ability to change its wearers form, and used it to defend the two planes from harm as the (Kamen Rider Monster). However, nopony can live forever, and eventually he has to choose a successor. And so it went, but after centuries, things calmed down, and the need for the Monster lessened. However, this could not last.
Under the first hoof, there are the Masked Knights. Wearing crude imitations of the Mask of Power, these Knights are dedicated to defend Equestria by any means they see fit, including the destruction of innocent life.
Under the second, an old enemy has returned. The Dragon King seeks to leave the confines of the Everfree and take all of Equestria, and seeks the followers to do it.
And under the third hoof: The mare who won’t either of these future’s come to pass. A mare who will fight the darkness with her very heart and soul. That mare… is Fluttershy.
Once a simple gardener, Fluttershy was perfectly happy to live like a normal pony, but when she was given the Mask by Angel Bunny, she was catapulted into a new life of adventures and horrors.

Fluttershy can transform into four forms. The first, her default while wearing the mask, is an ancient alien warrior from before the dawn of time itself. Something resembling a primate, with two arms and two legs and fingers. It is very agile, and the only form that carries weapons. Her second form is a combination of a bat and a pony, and a superb hunter. She can hide perfectly in the night, and manipulate sound. Her third form is a giant pony, several times that of a normal one, with grotesque muscles and phenomenal strength. Her fourth is Godzilla. Except yellow and pink. And it is awesome.

Fluttershy is based on Kamen Rider, which is something I only recently got into. Japonese fiction is always kinda wierd, but I hope I didn't dive to far.

So, Rainbow Dash loses the race and fails to create the sonic rainboom. Not only that, but because the animals just wander away from Fluttershy, she ends up lost and getting into trouble, which in turn lands Dash in further trouble with her parents. This causes her mother to double up on Dash, which Dash attempts to break away from by any means possible, which eventually landed her in jail. After climbing out of that mess, Dash tried a variety of jobs, settling on first responder. And to her surprise, she likes being a first responder. She gets to put her athleticism to good work, instead of just grandstanding for ponies. She has a job she loves, and good friends. Things couldn’t get better.
But then one day there’s problems. A call at the Weather Factory leads Dash to be exposed to massive amounts of Rainbow Energy, which is something I’m amazed I was able to type. This amplified all of her pegasus abilities to superequine levels. After waking up in the hospital and discovering these newfound abilities, Rainbow Dash decides… to keep doing what she was doing before.
One of the things about her series is that it’s not about super heroics so much as a look at how someone would really handle having super powers. She gets involved with super heroics as they become more frequent, but most of the time she’s doing her normal resque work. The conflict comes from blending the mundane and the fantastic together, and seeing how explosive the mixture is.

She's Equestria's answer to Superman. Again. All her pegasus abilities are enhanced, letting her fly at supersonic speeds, control air, and sense the most minor drop in temperature. Her strength and durability are also increased, allowing her to trade punches with Nightmare Moon herself. Not for long, but still.

Her stories are mainly slice of life, focusing on her relationships with her supporting cast. Her mother, also named Rainbow Dash, is one of the few Earth Ponies in Cloudsdale. She is taking care of her husband, who has Alzheimer's. Rainbow’s government liaison, Flash Sentry, and her get along fantastically, but a spot of UST makes thing awkward. Her best friend is Lightning Dust, who is secretly jealous and wants powers of her own. Her other friend, Thistle Whistle, is insecure and learning to be a better person.

On the one hand, I like the idea of a super hero the focuses exclusively on helping people, rather than fighting a super villain, causing massive collateral damage, keeping secrets from everyone, ectra. But I can't help but feel like this is kinda cliched, reading back over it.