I think you are missing a huge factor in the 3D gaming issue-- The online gameplay. Funny you should mention Descent, as I used to compete in Descent tournaments. I even won prizes and was invited to E3. Imagine that.
To this day Kali, one of the original online gaming services, still has a strong Descent community. I go back and visit on occasion, and I am always warmly greeted by people anxious to catch up on what I have been doing since I don't play Descent anymore. If I tell them what I HAVE been playing, they deride me for playing a "ground-pounder" (a game where the character runs instead of flies).
Indeed, I think Doom itself is retro. There still are many people working on and playing this game that it is silly. People on a few newsgroups ask for Rise of the Triad on occasion (not so much anymore since it has gone PD). Yes, people wax nostalgic for old 3D games.
The comparison between Doom and Doom III is interesting, and it really made me think. However, that analogy can be applied to any gaming genre... What is the difference between The Bards Tale, Eye of the Beholder, and Marrowind? Souped-up graphics and a minor variation in play. What is the difference between Gryzor, Nicky Baum, Sonic the Hedgehog, etc...? Same.
I like my 3D games (although I know I am the minority in this forum). Right now I am getting a great deal of joy out of SOF2 online. Maybe someday I will look back on it and become nostalgic, just as I sometimes do with my Descent days.
The major difference between old-school gaming and 3D gaming, I think, is the online communities that spring up around them...