I felt the same way about Wolfenstein 3D. The graphics were neat, but the game was a big step back from its 2D namesake on 8-bit hardware. It was just run and shoot and rub along walls hoping for a secret panel. I never understood why so many people wanted to clone it. Mostly the engine, I guess, because the game was just an ok design.
Doom, though, was amazing. It was a much more realized world, both visually and in terms of mood and design. Eventually the levels got a bit too puzzley, but it certainly deserves all the accolades heaped upon it.
This is a topic that essentially comes down to taste, but I'll attempt to outline the core appeal. You're right in saying that Wolf3D was mechanically simplistic when compared to the original - however, these choices were intentional. Carmack's engine provided a low-latency high-framerate simulation, albeit a relatively simple one. This was a fidelity in experience that was completely novel, so every decision was made to maximize the tactile feel of the moment-to-moment action. More complex gameplay elements were determined to be less of a priority if they a) technically slowed down the engine or b) kinetically slowed down the gameplay. This game was an appeal to the immediacy of the onscreen action, even moreso than the first-person perspective. Thankfully, this continued to be a core value for id, which is more than could be said for other shooters that offhandedly throw away input fidelity.
Doom, though, was amazing. It was a much more realized world, both visually and in terms of mood and design. Eventually the levels got a bit too puzzley, but it certainly deserves all the accolades heaped upon it.