Twilight: UW (Righteousness and intelligence) Rainbow Dash: RG (Timmy deck. Quick spells, some ramping, and then AWESOME big creatures.) Pinkie Pie: Mono Red (She's practically a chaos god. What else would she be?) Apple Jack: UG (Stalling the game with fogs and counterspells, waiting for just the right time until she can get her MASSIVE creatures out and wipe the board clean.) Fluttershy: GW (Token deck, getting plenty of little critters out there to help her and then swinging with her massive army!)
Celestia: Mono White (amass her army, and exile any opponents' creatures. *to the moon*) Luna: BW (Crusading against her offenders with vampires, knights, and spirits to slowly torment and dwindle away at them.)
Trixie: RB (Tru on that. Flashy and erratic, trying to win at any cost.) Zecora: GB (All about using her graveyard to her advantage, scavenging what she can get to find exactly what she needs to beat you.) Spike: Blue Fatty Aggro Deck because Spike is the worst character and doesn't know what he's doing. Shining Armor: RW (Lots of soldiers, burn, and anything to just hammer away at his enemy.)
I agree with all of those except one... Spike will have vengeance. With Slivers.
Also, Rarity would probably have a mainly artifact-based deck or something. And Discord is aggressively manipulative, so I can imagine a combo of Red, Blue, and Black working well for him. Or just Red and Blue.