Let's see... Twilight, as the Element of Magic, would be probably combo/control, winning only after long and careful preparation. Blue/White, most likely.
Applejack, as the Element of Honesty, would use no tricks, just pure midrange. She's probably most physically powerful, so Red/Green, which also corresponds to the green trees and red apples. As a farmer, she could make use of various green ramp spells.
Rarity, as the Element of Generosity, would be definitely a group hug in commander, but I'm not sure what she would do in duel.
Rainbow Dash, that's pure aggro. She's all about speed, so her deck would be about winning as fast as possible. Blue/Green, based on blue fliers and green pumping should fit her. Possibly blue/black since she is very self-centered at times and she's quite assertive.
Pinkie Pie doesn't really care about winning, she is just random and funny. That means probably mono-red or blue/red deck which tries to confuse the game state as much as possible via things like
Confusion in the Ranks,
Grip of Chaos, etc. -- and while the random effects mess up opponent's plans, Pinkie accidentally wins through
Chance Encounter and various coin-flipping cards. Pinkie could be also concepted as a mill deck because she usually doesn't win by overpowering her opponent but more like by tiring them out.
Finally, Fluttershy. Her deck is definitely green/white, with her ties to nature and community. Fluttershy is not aggressive at all, so her deck could be very defensive control with
Ghostly Prison, etc.
Epic Struggle would be a great win-condition for Fluttershy with all her animal friends.
The Cutie Mark Crusaders could have a goodstuff deck with all five colors. It could be great if it comes correctly, but it wouldn't be extra-cohesive -- they are chaotic when together and their plans work as often as they don't.
As for the main antagonists:
Nightmare Moon - blue/black, definitely, with nightmare theme (
Torment nightmares, possibly Ashiok as well).
Discord - like Pinkie, but worse. While Pinkie would work as blue/red, Discord is definitely black/red. Madness would be a good theme.
Queen Chrysalis - as a changeling, Shapeshifters are definitely a theme, both smaller Lorwyn changelings and various clone effects. Blue is a must, and as a secondary color, I'd actually use white. For one thing, it would give the deck access to
Crib Swap, which would be a fun flavor, but also, white is almost required for anyone who is a monarch (even Marchesa picked up white). But there's still lots of black, so I'd say that Chrysalis is Esper.
King Sombra - the Sombra from the show is basically an eldritch abomination, so black with powerful Eldrazi seems good. With the character development from comics, Sombra might even lose his black in favor of red as he's guided by his emotions a lot.
Lord Tirek - mono-black, as he cares about power and nothing else. Master of
Drain Life effects.
Starlight Glimmer - her community/cult building would make her white/black, which would fit with the
Starfield of Nyx deck I suggested.
And finally:
Celestia - as the ruler of the whole land, it's only appropriate to give her a domain deck using all five colors to good effects, although white would, of course, be primary.
Luna - Red/white seems nice for her. Why? Well, white corresponds to her dreamwalking and protecting of other ponies' sleep, and red is her emotional instability that led her to things like creating a monster for the express purpose of torturing herself. But more importantly, red has some moon-related cards like
Blood Moon or
Moonhold. Or, extend to green as well and let her use Werewolves with their lunar addiction problems.
Posted: 05 Sep 2016, 14:46
more with 
Your comment made me kind of curious what deck styles the main characters would then correspond to