Joffrey completely deserved it, of course, but try telling Cersei that. Instead, showrunners David Benioff and D.B. Weiss explain in the Inside the Episode that the line was a callback to Season 1 as well.
In George R.R. Martin's novels, Bran, Arya and Jon have all displayed warging abilities while they're sleeping, even if Arya and Jon don't consciously understand that they're inhabiting their wolves' bodies while they dream.
With Nymeria and Arya's reunion providing an emotional sucker punch in "Stormborn", perhaps another wolf scene felt somehow redundant when the episode was being edited?
Adding, "To be someone's pet would reverse everything she's learned. So they nearly just regard each other and go their separate ways".
Arya had just hear her half-brother Jon Snow had been reinstalled at the family seat of Winterfell, and viewers were in for another nostalgic moment when she found the direwolf she had been given as a puppy. Does that mean she could be ready at some point?
Will we see Nymiria again? As EW points out, the show doesn't show the direwolves very often in part because they're hard to convincingly render - we know what wolves look like, unlike dragons, so the team has to expend more resources to get them to look realistic.
Arya sees Nymeria for the first time since season one. "Since we last had Arya in the Riverlands she's had all these insane adventures". In a television show that's all about Nymeria the Wolf, she's had adventures too. "Then she realises the wolf is doing exactly what she would do if she were that wolf".
Interestingly, did Nymeria's reappearance also tie into this season's "lone wolf" prophecy? With that in mind, she could decide to go back on her original path and head down to King's Landing to kill the queen. "And that might be foreshadowing for Arya too".
People grow up and grow apart - the same is true of direwolves.
Hot Pie, another surprise returning character, told Arya that her brother (really cousin, but she doesn't know that) Jon Snow is alive and well in the North, so she chose to change course and head for Winterfell instead of King's Landing.
The scene in question saw Arya surrounded by a pack of wolves, only for a familiar looking face to confront the sword-swinging Stark.