You expressed it very nicely, sorceress. I had similar feelings when I played the game ages ago, but never managed to put my finger on it. To date I can barely remember the designs of most E2 levels – they are like a blur in my mind – whereas most E1 I remember quite well. E3 is a little better in this regard, but not as good as E1.
All E1 levels except E1M8 where designed by John Romero, whereas none of E2/E3 where. Many of the things that positively distinguish E1 from E2 are straight out of his “design rules”:
https://doomwiki.org/wiki/John_Romero#Design_rules
I guess this shows you that his reputation as a master designer is at least partially deserved. :
)