These are 1-on-1 character pairings that have yet to be done in an episode for the show. (correct me if I got any wrong)
Episodes where it featured three characters don't count. (like Putting Your Hoof Down had Fluttershy, Pinkie Pie and Rarity. on the other hand, some episodes featured a third character but she wasn't a main focus, like Look Before You Sleep)
Applejack and Pinkie Pie
Applejack and Fluttershy
Fluttershy and Pinkie Pie
Pinkie Pie and Rarity
Rainbow Dash and Twilight Sparkle
Rainbow Dash and Rarity
Rarity and Twilight Sparkle
Fluttershy and Applejack (redundant)
Pinkie Pie and Applejack (redundant)
Pinkie Pie and Fluttershy (redundant)
Rarity and Pinkie Pie (redundant)
Rarity and Rainbow Dash (redundant)
Twilight Sparkle and Rarity (redundant)
Twilight Sparkle and Rainbow Dash (redundant)
redundant = been mentioned in vice-versa before, made them smaller because you can skip them over
I'd like to see a few of these done, and am actually surprised one or two haven't been done yet.
I expect a few of these in Season Three now.