CAUTION: SPOILERS AHEAD!

First of all, I gotta say that I liked romantic chemistry between og Naksu (played by GYJ) and Uk way more than when she was played by JSM. And I liked that the overall story ended on a happy ending, which it desperately needed after part 1's devastating ending. For these two factors I'm willing to forgive a lot of things that were done quite sloppily in part 2, for example:

1. Dragged out FL's amnesia plot and repetitive misunderstandings.
The villains took a bit of a back seat this time around, the main course of part 2 was rekindling the relationship between the leads who, due to FL's amnesia and different looking body, couldn't recognize each other. Very cliche, but not a bad thing in itself. However, for 8 episodes straight the plot was basically going around in circles like this:
-ML says something cold and nasty to FL,
-she gets upset and leaves,
-ML regrets his harsh words and runs after her,
-they reunite until ML has another bout of unjustified cruelty towards FL.
Only in the last 2 episodes the plot finally kicked into high gear and the good guys swiftly, if a bit hamfistedly, dealt with all their problems.

2. Most characters' intelligence got dumbed down compared to part 1.
For the sake of dragging out the drama and misunderstandings they were frequently shown unable to add 2 and 2 together and unable to finish their line of thought when suspecting someone.
-For example, ML, who was very bright and quick to catch on in part 1, in part 2 couldn't figure out that FL is Naksu even with heavy hints given to him since part 1. He couldn't even catch on immediately after she basically spelled it out for him and showed her blue eye marks.
-Another example is Jin Mu immediately recognizing Naksu's face, but not investigating this very suspicious occurence further after simply examining her aura and learning she's a priestess, not a mage.
And the list goes on...

3. Contrived new rules and plot devices that contradict already established lore.
Master Lee, the blatant writers insert, almost every episode kept sparingly throwing newly invented sh*t into the fan to keep the audience in suspence and characters scrambling. Some plot holes remain open because of it:
-Naksu for whatever reason disappearing from JBY's body (that even looks like her now) when she regains her memories, of all things. Why didn't she disappear earlier when she was Mu-Deok? Unclear. But in the end, even her disappearance turned out to be a lie and she simply took a back seat temporarily for Jin Seol Ran to fulfill her duty.
-The fire bird being the original reason Jinyowon was built - no mention of it whatsover in part 1. Was this bird the cause of drought 200 years ago? How was it even captured? Nobody knows...
- The previously established lore stated that only priestesses with divine magic can perform the rain ritual and that it is being kept in Jinyowon. But no, apparently Jin Mu, a mage, had it ready all along and could perform it himself.
-200 years old Jin Seol Ran, who apparently didn't die as was mentioned in part 1, had planned this whole thing all along, so that Naksu and Uk could get together, protect the ice stone and defeat the fire bird, because she could forsee the future. I get Uk being the King's Star with superpowers, but why the heck JSR needed Naksu's soul stuck together with hers in JBY's body still remains unclear.
And the list goes on...

4. The villains overstayed their welcome.
Jin Mu, a very cautios and clever villain in part 1, in part 2 turned into a tired cliche of a tropey mustache twirling, maniacally laughing villain. But his schemes somehow kept working because the good guys, as was mentioned above, were intellectually dumbed down and kept being unmotivated to finish him off until the very end. No smart shaman this time around to boss him around, so he had to contend with dumb sidekicks, creepy crazy queen and greedy grandpas who wanted to live forever. And they all died like total dumbasses, because they grossly underestimated ML's power.

5. Naksu never regained her mage powers.
No badass Naksu expertly wielding sword and magic from S01E01. In the end she was lucky enough to stay in JBY's body through JBY/JSR's grace and kept that body's divine powers, which turned out to be pretty lame, compared. But at least she survived, I guess that's a win.

6. Promised indepth exploration of side characters' stories was a lie.
Most of the time was wasted on retired Park Jin cooking "black matter" to everyone's dismay, while much needed screen time for characters such as Park Dang Gu and Jin Cho Yeon was cut to a minimum. Even Crown Prince got overshadowed by a turtle, of all things.

7. Cheap fake deaths for drama's sake.
In the end none of the good guys died, the audience got duped again just for cheap nail biting thrills. This lessened ending impact by a lot, as the stakes turned out to be pretty minimal. But at least master Lee did something useful for once.

8. ML's reactions to learning that FL is Naksu and that she'll soon disappear were underwhelming.
I dunno what happened to LJW there, but I wasn't feeling any impact from those scenes and he didn't look emotional enough. He looked more like blank faced Yul, but even Yul was more emotional when he learned FL is Naksu.

9. Last episode was a bit rushed, erratic and weirdly edited.
Technically, on paper everything was done right, but somehow still left a feeling of being rushed.
I dunno what it was, but I think it's was an amalgamation of these factors:
-Weird, out of order editing;
-Erratic characters behavior, especially the villains;
-Lackluster CGI, baffling lack of extras in fighting scenes;
-Lack of impact in general - endgame buildup was ruined by ML who, after finally accepting his destiny of a total Mary Sue (aka. King's Star), practically singlehandedly smashed all the villains and that overhyped fire bird as easy as pie without breaking a sweat;
-Too much focus on side characters' endings instead of the main leads and even those were of barely satisfactory length.

Also, I think that leads wedding should have happened at the end of the story when all the issues were resolved, not when FL was about to disappear. It looked out of place considering their current circumstances and reminded too much of part 1 ending, when they were in denial and carelessly making future plans and marriage.

CONCLUSION:
So, did Alchemy of Souls require 2 parts for a complete story? Personally, I don't think so, part 1 already suffered from pacing issues, but in part 2 they've dragged the plot out even more and added lots of new plot holes, to boot. If the writers kept the plot tight, I think they could have ended the story in one season.
But then again, I really liked GYJ's Naksu character and I liked that she too got plenty of time to shine, like JSM did in part 1.
All the rest of the cast, LJW especially, did a really excellent job as well and part 2's overall production value was still through the roof.
Flaws and all, Alchemy of Souls is still a very memorable and gripping kdrama, with a beautiful love story, that I'm sure will be remembered for years to come as a great classic. There's nothing quite like it in kdramaworld right now and I hope it will be an inspiration for more quality dramas like this. Overall, I'm giving part 2 a generous 8 out of 10.