They are not on the same level since Duke Nukem 3D is a more advanced game released 2 years later but with which one did you have more fun playing? Duke Nukem 3D's most difficulty was Damn, I am good and it was quite a playable difficulty. Not really so hard but Doom 2's Nightmare was a real nightmare. I couldnt pass level 9. I like both very much but Doom 2's Nightmare is a stupid difficulty. Ultra Violence will stay as the real most difficulty for the game.
I dislike final doom, by the way. The maps are so big and boring. But Doom 2: Hell on Earth was awesome. It was the best classic Doom game for me. I like Heretic as well but didnt like Hexen much.
I'd say Doom 2, the maps were really big and all the sub floors and buildings. Plus there was some cool chest areas where I remember opening a wall and you were playing Wolfenstein. But tbh I never got into duke nukem.
Duke Nukem 3D had Titties, Catch Phrases and more flash. That was more appealing to me at the time of my budding adolescence.