Anticlimax Boss: The bossfight against Drakan can be won in less than a minute if you spam him with throwing axes (in Normal difficulty, you can carry enough of them to do it without going in mêlée range), then perform a series of Action Commands.
Magnificent Bastard: Freya, who's been playing you the whole time. When you kill Hel she breaks her promise to allow Skarin to seek entry to Valhalla. It doesn't end well for her since if she had just kept her promise she would still be alive and Skarin wouldn't have caused The End of the World as We Know It.
Scrappy Mechanic: While the combat was good and commanding your army worked well, the stealth sections where you have to infiltrate enemy strongholds are particularly annoying. There's no real stealth mechanic, you just have to sort of run from cover to cover hoping the enemies can't see you. If they do spot you (and they will, many times) every enemy in a very large radius will be alerted to your presence and confront you. Did we mention this was a game that could support hundreds of enemies, and they can all run faster than you? Mook Chivalry also does not apply to them, making detection certain death.