I played it through and it was very smooth. The level design was extremely creative and never unfair and well balanced. I never got stuck in the walls or anything like that, the controls are very precise. What I found is hardly worth mentioning...
In E1M3 I saw a gap under a path, looking out of a chamber that was blocked by a stone:
In E5M3 you walk at the top of the glass roof where the red key is against the invisible level wall. It was probably intentional, but a high fence would be better and the direct view of the entire skybox is not advantageous either:
Also in E5M3 there were two floating boxes outside the water (there is water on the right, not in screen):
For stairs, it would be nicer if the pattern matched the height of the steps so that each step looks the same. It's close but usually doesn't quite fit:
