In no particular order:
#1 – If Sam becomes Archmaester, what happens to Gilly and his adopted son and the son on the way? Are Gilly and the kids always going to be Sam’s taboo secret family, hiding in the shadows? There should have either been a line like, “Oh good, it was just decided that maesters can get pussy now” or Sam should have left the maesterhood and just become another kind of wise adviser – Master of Laws or what have you.
#2 – If Bran can see the future, then didn’t he know Daeny was going to burn everyone in King’s Landing and let her do it anyway?
#3 – Did Ellaria Sand get crushed in her cell during the dragon attack?
#4 – Is Daeny really dead? Keep in mind people come back to life on this show all the time.
#5 – Wouldn’t it have been better for Arya to become an assassin for good, using her faceless man skills to strike down the wicked? Or maybe she has learned the ills of revenge and is now using her family fortune to explore.
That’s all I have for now but feel free to pose your own in the comments, 3.5 readers.
Bookshelf Battle 
I like to think Dany’s dragon was flying her body to a reanimation pool he just happened to know about. Time for a Night Queen!
Also, I’m pretty sure Bran just uses Westeros as his permanent soap opera and he didn’t want the drama to stop.
Yeah its always possible Dany comes back and the Unsullied are so loyal to her that they’re only a raven message away.