The biggest one being a subject many times is to kill Paarthurnax or be denied/shunned by the Blades even though they are sworn to fight for the DragonBorn and you are the de facto leader. So yeah, Paarthurnax has done bad things because he and other Dragons had no other thought pattern in there minds to do so otherwise while under Alduin's influence. But whatever Paarthurnax has to pay! Even though he helps you fight Aldun! Meanwhile Odahviing gets off scott-free. Yeah, dont mind the fact that on the encounter with Odahviing he swoops in and grabs a helpless city guard in which he tosses 200 yards off the castle wall. Its all good with Odahviing though since he is willing to fly you up to Skuldafn on his back (something Paarthurnax could also do, but no option for that.). So Odahviing lives because he allows himself to be a flying transport in return to be set free, (aka Odahviing cut a deal to be set free and sold Aldun out.). Paarthurnax broke free of Alduns control durning the Great Dragon War and tought the Thu'um to mortals to help defeat Aldun and other evil dragons. Paarthurnax helps the Dragonborn in many ways during the game. Paarthurnax must die and Odahviing does not. THE END. stupid.
Olaf One Eye. He is a Draugr found in Dead Mens Respite (Draugr are men who once served Dragons and are not aloud into Sovngarde because of so.) And yet Olaf One Eye is also found in Sovngarde??? How could Olaf be made out to be a traitor, cheat, and liar. And have the quest for the Bards that uncovers all this and shows he is a Draugr yet he is also in Sovngard? Maybe there was a imposter Olaf One Eye? Or one good and one evil? stupid.
Companions and The Silver Hand. One group are Werewolves and the other are Werewolf hunters. The werewolf hunters are bad! Ok, I get the fact that the "Inner Circle" of the Companions are in full control of themselves in werewolf form. But they seem to be the only ones. Pretty much all of Skyrim view as werewolves as being bad. Because they are. You dont come across friendly NPC werewolves in the wild. The ones in cages in Silver Hand lairs will attack you if you set them free. You have a choice to kill Paarthurnax or not but no choice kill the Werewolf Companions? stupid.
Where is the moral ground here in Skyrim??? You have to kill one Dragon that has helped you and all of mankind and another one gets to live because he made a deal with you. You can lie, cheat, steal , and still get into Sovngarde. And werewolf hunters the bad guys.