You think Arya is getting Nymeria back?
Can it be proved that Weese's bitch was not a semi-mythical beast in the first place? Wait, don't answer that.
The above is all conjecture, but your third point is right along the lines of one of ASOIAF' major themes... fidelity.
The bonds of loyalty and obedience are strongly put upon the denizens of Westeros. Crown, house, region, fraternity, and religion all vie for people's ultimate loyalty. A person may be born into loyalty, but that person may choose to switch allegiances... and sometimes is even encouraged to switch by his own family.
To remain in good stead with the Iron Throne, Lord Tywin, Cersei, the Kingsguard, and the Church, Jaime has had to make numerous choices. He told Catelyn, "So many vows... they make you swear and swear. Defend the king. Obey the king. Keep his secrets. Do his bidding. Your life for his. But obey your father. Love your sister. Protect the innocent. Defend the weak. Respect the gods. Obey the laws. It's too much. No matter what you do, you're forsaking one vow or another."
Barristan, Jon, Jorah, Arys, Jaime, Tyrion, Robb, Roose, Theon, Aemon, Mance, Renly, and many others have their vows and oaths put to the test. This can be summed up in Jaime's next to last chapter in ASOS...
"It's not Ser Donnel the Constant who concerns me. It's you." Jaime leaned forward. "What will you do if brave Ser Donnel give his sword to yet another usurper, and one day comes storming into the throne room? And there you stand all in white, between your king and your blood. What will you do?"
"I... my lord, that will never happen."
"It happened to me," Jaime said.
Swann wiped his brow with the sleefve of his white tunic.
"You have no answer?"
"My lord." Ser Balon drew himself up. "On my sword, on my honor, on my father's name, I swear... I shall not do as you did."
Balon swore to kill his own brother if he defied Tommen. The Old Bear and Jon stayed at the Wall while their kin were murdered at the Twins. Arys forsook his vows and followed Arianne into treason. Victarion swore to himself to kill Euron, but ended up serving him. Who can say what allegiance Arya will adhere to when push comes to shove?
Ever since the moment that Ser Meryn Trant came for her, Arya's allegiances have been only for her survival. Her friendships with Gendry and Hot Pie and her relationships with the killers Jaqen and Sandor were about survival. You could argue her last demand of Jaqen served House Stark... but it served her as well.
Jon has learned repeatedly that his allegiances to House Stark are done with. He is a man of the Night's Watch body and soul. He's bled for them. He's killed for them. He's lied for them. He's forsworn himself for them... and he's returned with his allegiance intact. What will he say to Arya when she asks him to assist her in revenge? He'll stay troubled and keep his vows, ******* that he is.
Arya, if she holds any affinity for House Stark after her indoctrination in the House of Black and White, will not graduate. The old man has some supernatural ability to know her mind... She'll stay as an acolyte or become a practice target for a more devoted student. If she graduates, I believe that Arya will put the interests of the Faceless Men above those of House Stark.
I spoke above of loyalty. Loyalty breeds obedience. How can Arya be obedient to Jon, Sansa, Bran, Rickon, Brynden, or Jeyne if she possesses no loyalty to them?
It seems that the Stark children have stronger ties to their direwolves than Dany has with her dragons. Mayhaps this is because they have one pet each while she must divide her attention and efforts between three. Mayhaps this is because dragons are larger, more intelligent, more magical, and more indpendent than direwolves. It seems from the Dany preview chapter of ADWD that the dragons are on the brink of being beyond Dany's control. This might make it easier for a Faceless Man to turn one on Dany... also this might make it impossible for a Faceless Man to even begin this process. I dunno.
Just rambling thoughts.