I think most people find S1 better is because it related to the personal stories of the characters so there was more aggressiveness and anger in there.
Their approach to S2 wasn't bad. Most of their stories got resolved in S1, and in S2 they do show that Do Gi still has his trauma & how Go Eun is also trying to move on (with that episode of that religious cult and how two sisters were separated ). They didn't show much, and wanted to tie majority of the cases to the Bishop's organization which is fine.
The unrealistic elements in this drama has always been there since S1, it's just for entertainment and no need to throw logic into each situation. I like how they tried to make this more comedic and lighter whereas in S1 it was slightly more dark. I also think the Prosecutor Kang Hana role in S1 was slightly annoying. The revenge never disappoints though. In each case, the villains get what they deserved.
I felt they tried to make the Black sun similar to burning sun which I'm glad they covered that.
The cameo role for KSY was interesting. But it also feels random that they threw in first taxi driver in there. It just makes me wonder how long this deluxe taxi has been going on for.
As for the cliffhangers, I really wish they wouldn't leave off a cliffhanger unless they planned for S3. They just left a case hanging in the end. I think it was a nice case too since it does happen in the military.

There was obvious product placement in this season. I didn't mind it, but wish they would cut it down a little. I think showing the coffee candy once was enough, same with the tonic.

Acting- They all act so well. LJH acting as a country bumpkin or something else. We saw so many different sides. I was skeptical about SJH's character, but he did good too. I felt some pity for him in the end with that plot twist.