SkunkyArt | RoboTheHoobo — MLP - The Justice Elements

Twilight (MDW)- Definitely fits with MDW. While most of the group played a role, Twilight does seem a likely candidate for Mare Do Well. And given her ascension to alicorn, Twilight being MDW would make it extra awesome. (Not to mention nopony, or author, realized the oddity of a pony wielding all powers of three pony races.)

Fluttershy: Her moments where she had to be stealth operative of the group and does pretty well.

Rainbow Dash: The popular and favorite one. The Flash fits Dash in her speed and loyalty towards others. You could argue that Dash has her own group like Flash. Her Reverse-Flash being Lighting Dust (especially now that she has THe Washouts), and her Kid Flash being Scootaloo.

Pinkie Pie (Pinkie Pool): Pinkie fits in being the oddball/wild card of the group. While nowhere near violent like Deadpool, she definitely fits his title of "Merc-With-The-Mouth." She also is good with kids.

Applejack (Vigilante): being from early days of American superheroes, the original Vigilante costume fits Applejack

Rarity: not revealed here, but I suspect her identity as Radiance (Power Ponies), who is an Expy for Green Lantern. Given her current fate in part 2, I think its a likely idea.