Nobody ever said that DNF was equal to HL2. What I said is that they share a lot of similar design choices. Namely, the lengthy intro sequence, the puzzle and platforming segments and the lengthy vehicle segments. Many of the people who criticized DNF did so because these elements existed, not because they were poorly done. These same people praised HL2 as one of the best games ever made.
People criticized the inclusion of those elements into the game because it was a Duke Nukem game. No one was saying those elements are universally bad (as in, they worked fine in HL2), they just didn't belong here.
In Duke Nukem, you shouldn't have to have a long, lengthy intro, because you play the game to jump right into the action. That's the style of DN3D, and should have been the style of DNF. Having a lengthy intro to HL2 worked (and worked in HL as well) because they aren't instant action games, they are slow build-up games. The same disconnect is true for platforming, and to a lesser degree, vehicles.
Just because something worked in HL2 doesn't mean its inclusion in another game is going to work, unless the style of the game is also similar to HL2. And despite them both being FPS, the styles of the two games are nothing alike.