Part 1 of this drama was one of my favourite things I ever watched. The characters were well-defined, and the story flowed perfectly. Everything made sense and tied well (and very tragically) at the end.
While I still enjoyed part 2, and while I liked the direction of the story in part 2, most of it was really frustrating to watch. Here are some of my reasons:
[SPOILERS WARNING!]

1. Master Lee
His character was absolutely charming in part 1. I loved how he subtly helped Jang UK reach his destiny and always looked after both of them. But in part 2, his character only seemed to exist just to confuse us and throw us off, so when the real predictable plot happens, we'd be surprised.
In one episode, he says that Bu Yeon is dead, only to reveal two episodes later that, nope! she was actually alive all along...
And then he tells Yul about this big hard choice that UK will have to make between saving Naksu with Hwansu or doing the right thing, but we never saw UK make this choice or even consider it ever?!
Don't get me wrong, it would've hurt to see him make this choice and I'm glad he didn't, but why foreshadow something that was never relevant?

2. Jin seol ran
The whole "She was actually Jin seol ran all along" seemed irrelevant to the plot. She didn't help them like...at all?
Except at the end with the basin but that was after the bird was free and the world was already on fire?
But even then, if the writers went with her being Jin Bu Yeon it would've still made sense. It seemed like an unnecessary added layer of confusion.
If she foresaw all of this, then why didn't she give them a warning? why did she hide in Sari village all this time?

3. Naksu
The memory loss plot realllllyyy dragged. Jang UK seemed to be made slow this season just to stretch the plot. He was really smart in the first part, and I refuse to believe that it took him this long to connect the dots!
Part of why we fell in love with Mudeok was her ruthless, fearless character who had a warm side to her, but she found it hard to show. I didn't feel those characteristics in the second part. Regardless, I think Go Yoon Jung did a great job, and at times I felt like they really were the same person, but those times were rare.
Stretching the memory loss plot robbed us of seeing the Naksu we knew because everything that happened after her regaining her memories felt really rushed. It felt like Mudeok completely disappeared once part 1 ended.
The final scene when she was telling UK that she doesn't want to train anymore felt so detached and out of character from the Naksu we knew and loved...

4. The time jumps
I would have loved to see a little bit of the aftermath of what happened at the end of part 1. 3 years gap was a bit long.
And then again in the last episode, they had a 1 year jump out of nowhere.
One minute we were fighting the firebird the next, we were babysitting Dang-gu and Cho-yeon's babies. From a super intense scene to a super colourful scene. In fact, most episodes had this sharp transition between the scenes. Similar to how 3 main characters died in one scene and were brought back literally 30 seconds later. It felt like a lot of the plot this season was done and then undone over and over again.

Overall, I still loved and enjoyed this drama, and I will dearly miss it. My favourite thing about part 2 was the cute romance since we didn't get to see much of that in the first part. The actors/actresses were great, and the soundtrack was amazing. Weekends will truly feel empty now that this drama is over.