alright changed AJ and RD  
AJ is a Ground Attacker who can’t hit Aerial Enemies and Rainbow is an aerial attacker who can’t hit grounder enemies as well as AJ but can do well against aerial enemies

alright  
MC: Twilight  
Sidekicks:  
Spike (Tattle)  
Rarity (Shell/Gem Def)  
Rainbow Dash (Attacker)  
Fluttershy (Multi-target attack/Support)  
Applejack (Heavy Hitter)  
Pinkie (1 Turn Invincibility ie Vivian and Bow)
 
Villains: Trixie, Gilda, Diamond Dogs, Chrysalis  
Main Villain: Nightmare Moon/Discord (pick one)

My idea would be like, if Twilight Sparkle is the main protagonist, Trixie could be like a rival that keeps coming back to fight to prove herself against Twilight.  
 
^Heck, he gets magic by the end of the game. :P

@Candrew:
 
>Trixie is a one-shot antagonist
 
NOT FOR LONG!
 

^ I could also put her as Tubba Blubba, made invincible due to big bad intervention until you figure out her weakness.

Nevermind, I support FlutterLove’s thing.

Trixie is Doopliss, she is going to try to take the main character role away from Twilight

We still run into the problem then that Trixie is a one-shot antagonist as opposed to one of the 6, 7 if you count Spike, main character protagonists.

Well, why should all the characters mirror perfectly? I would think that the style and gameplay elements of Paper Mario could be implemented, but restricting the personalities just adds an unnecessary limitation. On that basis, I stand by my choice.

^^ Two sidekicks also works.

Yes!

I can’t see Trixie as the main character in a Paper Mario game because Mario tends to be modest and quiet, while Trixie is…Trixie. Sadly, there isn’t really a great fit among the mane 6 for Mario’s role. Maybe, as much as I’m loathe to suggest it, Big Mac would be the best choice.

^I think a paper pony game shouldn’t have a mario character; there would just two “sidekicks” battling at a time.

I think Trixie should be the main character.  
I’m not just saying that because she’s my favorite pony, either. I think her bravado and slightly above average magical abilities would lend themselves well to a protagonist role, especially in a Paper-Mario-esque RPG. She knows enough to start out, but she still has a lot of room to grow and gain new abilities.  
That would also allow Twilight to fall into the sidekick role candrew outlined.

I’m torn on my opinion of this pic.
 
On the one hand, Twilight is clearly the main character, on the other she fits perfectly into the role of the sidekick who knows everything about the enemies and locations.

A Thousand Times YES!

I AM THROWING MONEY AT THE SCREEN, BUT NOTHING IS HAPPENING