Pinkie Pie vs. Shishio Makoto…
 
I can imagine Shishio slashing/burning the party favors being thrown. But she would win hands down, because her antics would make him overheat and boom spontaneous combustion.

Nightmare Moon vs. Battra. Two once great entities gone rogue fighting each other.

The Rage Virus being the genetically modified Ebola strain that creates the zombie-like infected of 28 Days Later and 28 Weeks Later.
 
So basically this:  
http://derpiboo.ru/81167?scope=scpef37f6aea4e25df229efa58134eecbfc8acc8057e

The Rage Virus vs. Fluttershy? It’ll be tough.

The Changelings (and by extention, the Dominion as a whole) from Deep Space Nine vs. Twilight Sparkle?
 
Easy: She gets her brother and sister-in-law to use the power of love to drive the Dominion forces from Cardassia Prime and the Alpha Quadrant, while she deals with !Pony Weyoun and !Pony Dukat (whom is now possessed by windigos).
 
Epicness = 8/10

sephiroth vs fluttershy

Oh god no,
 
Zsasz vrs the mane six.
 
This can’t end well :s

Dr. Breen vs. Fluttershy?
 
 
…huh. I think it’d be a stalemate.

Foxbat vs. Zecora… no idea who would win, but it would be epic, retarded, epically retarded, retardedly epic, or all of the above.

Rainbow Dash vs Dr. Nefarious…
 
I would pay so much fucking money to see that fight!

The Daleks win, because not even Discord can out-exterminate them.

Um…fuck! I can’t think of my favorite antagonist.

My favorite antagonist? Lieutenant Colonel Nicholson. Watch Bridge on the River Kwai. If you ever want to see a villain who is an actual, genuine real-life villain watch it. So, honestly? Nicholson would probably subvert the pony, take over his/her/its agenda, then outpace the pony in whatever he/she/it is doing.

Pinkie Pie vs. Handsome Jack?
 
I think I played that as a Mechromancer.

Rarity vs Shodan. Truly a battle for the ages. Realistically, Rarity would be hamburger in minutes, but since we’re already in the realm of insane (and awesome) fan wankery, I’m going to say that Rarity will win, by shaming the various horrific mutants and psychic monkeys for their atrocious fashion sense. And then she will merge with Shodan, and become the most awesome character ever created CYBERARITY! An unstoppable reality warping super computer devoted to making the universe fabulous.

The Devourlord vs Twilight Sparkle…
 
Twilight, I really hope he kills you because I’m too afraid to know what would happen if he decides to let you live…
 
Devourlord: Elements of Harmony Battle Royale! Winner gets to see their loved ones live another day…maybe…

Wait, I thought this said ‘anatgonist from the last movie you saw’. I have many favorites, so I have to split this into 3 categories.
 
As for amoral villains, Twilight Sparkle is fighting the Tyrannosaurus from Jurassic Park. If she doesn’t use a magic beam or teleport, she’s bucked.
 
As for minor antagonists, Twilight Sparkle is fighting Trixie. This would go just like Magic Duel.
 
As for totally evil villains, my beloved mare is fighting AM. If that pile of circuits lays even a single wire on her fur…

Favorite villain right now is…  
 
GET THE ELEMENTS!

The Didact vs Applejack? Oh man, I hate to say it, but I think that the Didact would win.

Omega Zero vs Applejack.
 
Run, AJ, Run!

Rarity against The Master.
 
Epic.

Kyubey and Alfred Bester vs Rarity?
 
This is going to be the least physical battle ever. XD

Bowser and Princess Celestia eh?
 
…Things should go fine.

Rarity vs Dark Kazemaru?  
 
At least make her discorded so she steals his alien stone  

The Anti-Spiral versus Twilight Sparkle?…Oh shit. Hot damn.