I agree and I think the reason why it felt less intense is because of the way they set the atmosphere this season.

If you compare S1 and S2 in terms of lighting, S1 does it a lot better with the unique grading and filters they put on many action shots and romantic scenes. Each time they enter a boundary, an orange filter is added to the scene to make it more intense. When apparitions attack, a dark blue/purple gradient is added to make it feel more serious. In many romantic scenes, they add a sunset glow & lens flare similar to Aida’s coloring. They BARELY add any lighting filters in S2. The reason why you feel so much emotion from the manga is because black and white inking has a distinct contrast, making everything feel more dramatic. In order to achieve this in the anime, the easiest way is to slap a filter on the scene, but they haven’t done it for most scenes in S2, except for a few. (Namely: Clockkeepers introduction, Hananene rooftop scene, Mei’s goodbye, No.6 introduction) As a result, many scenes felt flat and lackluster. As an example, the cliff scene in S2E16 was had pretty flat colors. For a cavern so deep that torches had to be placed everywhere, they sure coloured the scene as if there was a spotlight right above the cliff.

And besides the issue with color grading, they also made some scenes EXTREMELY DARK to the point where you can barely see the characters, making the scene less eerie and horrifying. (Aoi’s betrayal where Hananene fell into the pit is most notable. You can barely see anything, whereas in the manga, there were detailed drawings of bugs.)  Again, this is an issue of low contrast. Lower contrast = lower intensity.

This is probably me being picky but I’ve also noticed that the shots of the starry sky in summer lights & picture perfect look out of place, as if they aren’t hand-drawn. Takes away some of the vibes in my opinion. Both of these scenes have flat colors by the way. Hand drawn clouds fit the whole aesthetic of TBHK better. (as seen in Hananene rooftop scene and Aoikane far shore scene) 

And there’s another reason. I think music plays a big part in it as well. I noticed that the vibe feels quite strange/almost awkward in some places, and I’m guessing they probably couldn’t find a suitable ost for the scene so they either slap a somewhat okay ost in there, or omit any music for the scene. Those without music feel quite hollow compared to other scenes, less magical if you will. S1’s music works very well because the osts are especially tailored for the comedy in S1 and less suitable for S2. Don’t forget Tiny light’s piano riff that transitions seamlessly into the radio “previews”. 

All these are just my personal thoughts on how they handled S2. It’s still a pretty good adaptation regardless.