So the last one and the toughest! It was so hard to do this, because other than in the last two video, this video referred to love! I thought about Fluttershy first, but since Spock is Twilight and AJ and Twi share more scenes together, I ended up using her. I also think Applejack is very much like Uhura, so it fits. Pinkies last appearance as bad guy. :( She´s done a good job admit it! xD OH and here would be my idea for the Into Darkness cast:

Kirk= Rainbow Dash
Spock= Twilight
Scotty= Spike
Uhura= Applejack
Carol Marcus= Fluttershy
John Harrison= Pinkie Pie (don´t ask why, she´s not like him AT ALL!!! My mind is crazy!)
McCoy= Rarity