While I didn't think season 1 was a masterpiece at the time since it did suffer of some plot problems in terms of explanations and execution, it is a masterpiece if compared with season 2.

Season 1 had a very good setting and a motive, even if somewhat very generic and never explored enough in my opinion.
I still don't really understand the reason of creating the monsters, evolution or some powers is not worth the hassle, especially from a capitalistic standpoint, they lose more than they gain, immortality might be the only real perk here but potentially killing everyone around you when you cut your finger with the kitchen knife is not worth the immortality in my opinion.
The motives of the bad guys are never fully explained and fall into the very generic category, either just because or because wanting to save X person.

Season 2 main problem is the plot and its execution. First of all like many others have said there are way too many plotholes and I don't think they'll tackle them in a potential season 3. They had the time to show things but they didn't. Of the 7 episodes about 4-5 are just a mess of getting back to the point where we were at the end of season 1, sprinkled with some flashbacks that didn't add much in terms of explanation of the most important things. We're not even told fully well what happened a year prior, nor how the relationship of ML developed with Seung Jo, we're told a bit but not shown. This is a repetitive occurrence in this season, we're told things but not shown.
The setting in season 1 was interesting both historically and cinematographically, here it completely lost the charm it had between the warm tones and the grittiness of the hospital and changed to just dark. Someone please turn the light on!!! This is a problem in many Hollywood productions nowadays, they're recorded very dark to the point at moments you can't tell what is happening in the scene, here they used the same idea and butchered the balance it previously had.
The monsters are very underutilised. There was a reason for it to be there in season 1 because of FL's mother and the general plot, here it feels like they were put there at the end for the sake of not receiving complains there were none, but nothing more. I still don't know more about these creatures than I did in season 1, they seem to be conscious to a certain extent so why would they do what their captors want anyway. I'm a monster and instead of attacking whoever is being put there for me I would just continuously try to break free and kill who did it. Season 1 certainly had more nuance in this aspect but season 2 seems to have gone backwards.

One of the things that annoyed me the most about season 2 is how background character they made the FL. Sure, she's there in body and does some cool fighting scenes but her essence feels pretty off most of the season and she was mostly relegated to damsel in distress. I still don't understand this, she's supposed to be better fighter than ML (sure, he has caught up in the years) and you would think that having her mother's najin (what seems to be kind of special in some way) would put her at an advantage over others, yet they made ML way more powerful than her and he's the one fighting all the bad guys. We're at no point told or shown what kind of najin he was given either for this to be this way. It was disappointing, even more considering that with her memories erased at the end they made her a girly girl??????? Where is this coming from!!!? ML didn't have his memories for a big part of season 2 but he was still mostly himself in his ways and personality (although generally not so much the same personality he had in S1), but with her she lost completely everything that made her herself.
I liked ML in season 1 because it felt like it was this somewhat cocky guy that found himself in a mess and was doing the best he could in the situation but here they decided to make him a superhero basically, and the main problem is not even that he's that way but the fact that we missed and are not shown how he got to that, he simply is now.

I don't have much opinion about their romance since for me it's just base ok, but repeating the plot and dragging their love misery gets old quickly, as in, it was already exhausted in the first season so I didn't want nor needed to see more or less the same love plot in season 2.
Seung Jo was very underutilised and the background stories of the other villains were also very nonexistent here. Can't even begin with those ninja najin mutants that had their heads covered. Imagine having extra good sight and covering your eyes just because of the fashion purposes of your master. Sir, you want the job done or aesthetics? I guess it's the second.
The action parts were good, but they were also dragged for the sake of it trying to show off. It almost reminded me of when I watched Aquaman, it's an action with some sprinkles of plot in-between and here it felt a lot like that too.
Season 1 certainly had more of a plot and there was more exploration of characters, they also felt all more unique. Here they become more the generic dichotomy of superhero series/movies bad guys vs good guys. Sure, they tried to make Seung Jo more of a grey character but with his background character very erased from the plot except for a few flashbacks that don't explore enough and don't let you connect with him, he's just a villain to all effects here.
I found the character of Lady Maeda interesting in the first season, if ultimately disappointing in her, again, dichotomy of character, but in season 2 is just plain boring and very background. I couldn't wait for her to die (if indeed she has that is) but once she did I even thought it was unsatisfactory considering the amount of stuff she had done.

Funny enough, despite all its flaws it's still entertaining at times and the reason for my rating. It's watchable as an action series with nearly zero brains in the plot, don't ask questions. I think if there is a season 3 it might be worse than this one, clearly they're going for an apocalypse type setting with mass killings, what means even more action and less brains.

I think if there is indeed a season 3 you can skip the 2nd altogether, you only need to know that FL and ML found each other and that she had her najin from the end of season 1 removed. Watch the 2 minutes prologue of the last episode of season 2 and you're set.