Rainbow Dash would be Raiden  
But the Shadowbolts would fit the Winds of Destruction more than her friends.  
The Mane 6 fit the og Metal Gear cast, anyway.
 
Twilight is obviously Solid Snake
 
Rarity is Meryl
 
Spike is Otacon
 
And Pinkie Spy would obviously be Johnny

“Here are 72 women to berate! The chocolate’s falling gently down on the train!”

@Daneasaur  
“Believe me, if they amputated your entire body from the molars down and this was all you had going for you, you’d make the time to pretty the hell out of your hair”

@Shepard’s Favorite Store on the Citadel  
Too true! I couldn’t see rarity going without her mane, no matter the body she had.

@Daneasaur  
Not to mention Rarity busts her ass to make sure her mane looks good, much like Mr. Lightning Bolt.
 
You’ve convinced me, Rarity the Ripper is the best option.

@Shepard’s Favorite Store on the Citadel  
That’s exactly what I’m saying. She hides parts of herself to fit in with “society”. We’ve seen she has a nasty temper and is actually VERY greedy if she allows herself to be. This isn’t just referring to Discorded version of her, but she did it in Dragonshy where she was more interested in the dragon’s horde than actually getting the dragon to leave. There have been several other situations where she valued something else more than what was socially acceptable and backstabbed all her friends to achieve it, such as with her stay at canterlot castle and when she got into high standings with Fancy Pants. True she righted her wrong, but she had zero qualms about doing it, she merely didn’t want to lose either one of the things she had.

@thps48  
The Hoops, Shaq!

@Daneasaur  
Rarity does seem to be two sided at times when really she could be both but her own standards and society wouldn’t allow for it.
 
By the time she were to face off against Monsoon she’d come to the conclusion that she was denying who she actually was and keeping an entire half of herself locked away for reasons that were hollow to begin with.

@Shepard’s Favorite Store on the Citadel  
“I’m going to cut you to pieces! I mean _{if that’s okay with you}?”

@Shepard’s Favorite Store on the Citadel  
Well, all of them have issues they wrestle with.
 
I likened Fluttershy to Mistral for being “cute” and attractive, controller of the “little guys”, and flips to kill mode in a heartbeat. whereas “jack” is something that is wrestled with, which I likened to Rarity trying to keep looking “fair and upstanding”, but she often wants to outright explode and cave into her vices, not because she feels bad when she is involved in them, but because they feel good.

@Daneasaur  
Personally I think that Fluttershy fits Jack’s bill the best simply because out of anyone she appears to have the most pent up/suppressed aggression similar to Jack the Ripper.

@Daneasaur  
Or Rules of Nature, Tirek certainly has the advantage in size in strength, but Twilight still beats him despite that.  
Unless you interpret the lyrics as RAY and GRAD lamenting that they’re not as pivotal in the Metal Gear universe anymore, then it doesn’t make any sense.

@Deserter  
RD also likes a challenge and would pride herself on being “faster” with as few “unfair advancements” as possible.
 
She’d also most likely see herself as the proper “rival”.
 
On another note: I still think it’s stupid as shit that anyone uses “it has to be this way” for the battle between twilight and tirek, as the song symbolizes that both want the same result, which is horribly wrong.
 
Collective Consciousness would suit it far better as he’s about subjugation and bending others to his will.

@Daneasaur  
I always saw Lightning Dust as Sam, but that was simply because I was trying to figure out who would fit better, and she was the first thing that came to my mind.
 
She definitely has the smugness and impatience down, though.

@Deserter  
I still see RD being more Jetstream Sam.
 
Also, Sundowner has the southern drawl to his voice, and is one of the few i could see as being brute force.

@Deserter
 
And still having the audacity to call Sundowner’s scissor sword “gimmicky shit” after all that.

@Sff  
Personally, I believe Dash fits more, if only because no one believes Raiden’s hair color is his natural one.  
Also, Dash seems like the only one that could think that judo flipping a giant robot, then chopping it’s arm off after running on top of it while it’s still in mid-air be tactically sound.

@Sff
 
“It’s time for Applejack… to let ’er rip!”

@Daneasaur  
One could make the argument that AJ should be Raiden, so that she can be Applejack the Ripper.

YES!! For fuck’s sake, I was WAITING for someone to do this!!

 
I’m surprised it took me so long to make the connection.

Oh my god, this is perfect. XD

I knew it! I knew someone would make this edit! Thanks OP!