I have to agree with a few that have been mentioned... the crazy container capacity (although maybe they found a way to duplicate Hermione's ever-expanding bag

), immortal NPCs, etc...
Mine, it has to be the main quest's climix, namely...
Spoiler Sovngarde. No one living should be able to get there, PERIOD. Add to that the fact that this is specifically a Nord belief, it made me do a

, since I traditionally play a Breton who doesn't believe in the afterlife. Yet... Tsun says my character will be welcomed back when he dies! Say what?!
I think the better way to do this would be to have the story end after the battle with Alduin. The dragonborn has to DIE to get to the afterlife, like everyone else, no dodgy magic. From there, we get an epilogue of sorts, recapping the player's deeds, both good and bad, similar to Fallout: New Vegas.
Now of course, I do understand it's a game, and just let it slide... this is supposed to be fun, after all. So that's what I do. Just let it go, and take it as it is: entertainment.