Well, yeah, all you said is true.
The problem with T4C is that it never went after the prototypal stage. You could run around in the existing (incomplete) levels, but I've never been able to add scripts to "make things happen", while this is a lot, A LOT, easier with the Doom 3 engine.
Also, I think Tommy is a more interesting character than Duke Nukem (or a Duke Nukem impersonator): he doesn't have "an ego the size of Texas", so he can express emotions like anger, frustration and fear, becoming more realistic. And with such a character, I decided that Altered Reality would not need to be a parody of anything. There would be citations and easter eggs in parts of the level design, but the story would be serious in tone (and not tongue-in-cheek like a parody would imply) and completely original.
In the same way, the next level will be set in a ghost town... but I bet that nothing of what will happen in my level will ever have a chance to happen in DNF.