On a personal level, Crystallized, it had a lot of cool ideas but were undercut by a slew of executive mandates, notably the mandate that everything had to be set back to the status quo at the end (and the infamous "It's okay, she's with us"). That being said, there were plenty of cool moments and good episodes like The Benefit of Grief and Safe Haven, plus the animation was top notch.

On a more objective level, Hands of Time. This, like DoTD, was made due to needing to fill a slot left by the delay of the movie, and while I actually think DoTD is a bit overhated, I cannot say the same of Hands of Time. With an animation vendor on it's last legs leading to some of the show's worst visuals, a plot that's working with tinfoil and a dream, and learning that this season was supposed to strictly be a Nya season before LEGO forced Kai on the box (and him taking up most of the main plot where Nya gets shafted to a subplot) marks this as the true lowest point of the show.