@Dawn Blast  
none of them fit Red.

Observe that none of them are Red…

The older version has been merged in per request.

Also, if anyone is looking for a good Pokemon manga, I’d recommend Diamond and Pearl Adventure!, and yes, it is with the exclamation mark. It’s been translated by Viz and finished a few years ago. It’s basically Pokemon meets early Dragonball, with kid Goku as a Pokemon Trainer. Really. It’s just as crazy at it sounds.

@PVRyohei  
If we’re going with Twilight - Platina, then we must have Celestia - Cynthia. Powerful mentor figures with long hair that covers one eye who gets defeated by a villain that should be normally be weaker. Also, both are depicted as memetic molesters.  
I can’t seem to think of any comparisons for the villains of either series, aside from Discord - Sird… Ghetsis - Chrysalis, maybe, but the former hasn’t revealed his evil plan yet in the manga.

I completely agree with Fluttershy/yellow, Rarity/Ruby and Celestia/Blue but I have different matches for the others:
 
Rainbow Dash - Gold - Both are fast (Dash flies, Gold has a scooter) and can be considered jerks with hearts of gold.
 
AJ - Red - I can understand why you picked Pearl, but I think he’s too hyper to be compared to her, while Red is a a far more level-headed heroic character.
 
Twilight - Platina - Both work perfectly for her, so there’s not much to say here.
 
Pinkie - Emerald - Pinkie is a really tough one. Dia actually fits, but he’s too lazy, so I pick Emerald.
 
CMC - Team Rocket Elite Trio (Ken, Ryo and Harry) - They’re both trios of recurring character who are always together, and never do anything right.
 
Luna - Silver - They are more serious, uptight characters. Green could also work, but Silver has his connection with Blue/Celestia, so he’s a better fit.

@Splinter17
 
500 chapters?
 
Oy vey.

Spike - Emerald  
Scootaloo - Gold  
Shining Armor - Red  
Discord - Sird/Storc/Saque
 
@Yorec  
It is good. There’s a reason why fans consider it to be THE Pokemon manga. Read it here when you get the chance.  
Grab some popcorn and soda, you have some 15 years, 43 volumes, and almost 500 chapters of catching up to do.

Also read Electric Tale of Pikachu if you haven’t in a while.
 
I’m sure you can find used ones cheap.

@RIG
 
Yeah Ash is actually pretty competent in this manga.
 
I like it. I have the whole first volume too. I should really see if I can find the rest on Ebay.
 
But yeah I may check this out. I hear Pokemon die though, not sure if I like that though.

@Yorec  
oh! that one where Ass Ketchup doesn’t suck and he is interested in girls (and his pokemon evolved too)!  
well, this one is pokemon adventures/special, the second oldest pokemon manga, is really good, is like the games with more story.

Okay it’s called “The Electric Tale of Pikachu”. It’s actually pretty good.
 
It’s by Toshihiro Ono who I later found out has done some Hentai manga.

@RIG
 
hold on let me go find it.

@Yorec  
by Viz? must be this one, what is the name of your manga?

So uh… how good is this Manga? Would anyone recommend it?
 
Its funny cause I never knew this one existed. I have this other Pokemon manga published by Viz I think.