I think Discord was targeting Twilight, either as his plan from the start or as a side effect of corrupting the others.Ookami-kun said:I think the reason Twilight wasn't trolled by Discord was due to her element being neutral (i.e. Magic)
Although Twilight's actual element is magic, I prefer to think of it as friendship (Twilight doesn't get the element of magic in episode 1 of season 1 until she realises that the other 5 are her friends, friendship is magic etc).
As McNum brought up earlier, by corrupting the other five characters Discord stops them from using their elements but also erodes Twilight's friendship with them and stops her from using her element. In fact, Applejack's vision (Granted it might be a complete fabrication by Discord, but to me he seems more likely to show the real future, probably way out of context, to influence someone or cause them to create the very future he showed them) might be the point where Twilight loses her element.