Hmm… I disagree.  
Pinkie as Tobi would fit better. Tobi/Pinkie is a goofball while Madara/Pinkamena is anything but.  
Rainbow would definitely be Hidan.  
I see fluttershy being more like Konan.  
Now Twilight, she might definitely be Orochimaru (though she’d have to get over her snake fear).  
I can see where you were going with Rarity as Deidara, but Sasori feels more befitting. She has mannequins, she makes clothing, etc…  
Applejack, the character who does nothing but love her family endlessly, is Itachi? Maybe… I honestly can’t argue for or against that. For some reason though, I feel as though Kakuzu is more fitting.

and who is Tobi?

Poor Pinkie got stuck as worst Akatsuki member.