Rarity should be black widow - glamour and clothes make the spy;



Rainbow Dash should be iron man - she flies, and her temperament reflects tony stark's;



AppleJack should be captain America - All-American pony;



Fluttershy should be Hawkeye - Living alone in a cottage out in the middle of nowhere?



Spike should be thor - A being from another world;



Not sure is Pinkie Pie should be the hulk - The hulk is a wild card of power for the Avengers. Same as Pinkie Pie being a wild card of fourth wall breaking for the Mane 6. But if Hulk isn't suitable, then spiderman would be a better fit.





And Twilight Sparkle as Vision.