So, it hurts a bit more the second time.
With the story and gameplay that this game has, a second playthrough where everything is sitting in the front of your mind is destined to be smoother. Items you had no thought in now aren't skipped over or stashed away, navigation and puzzles are that much easier as you've already seen the areas and solutions before, and those little things that didn't add up are staring you in the face.
Coming back to the start of the story after getting the sparse details it gives and connecting some dots around what it all means paints a different picture of what was going on... even if it wasn't exactly subtle in what it was originally setting up. It's blatant that this is a time loop story and having a full view of the mechanics and setting of the world makes everything even clearer. Which then leaves all the murky spots all that much worse when you still don't have that full a picture.