With a lot of games the first sequel is actually the best in terms of gameplay. The first game is usually testing of ideas and what not and by the second game they've learned a lot from their mistakes and successes. Most games series have their peak somewhere in the middle, the problem is that they keep going well past it.
In the PC Games thread I was just posting links to the early id games lineup and noticed that while Wolfenstein was the first, followed by Doom, Quake 1 was really 'it' in terms of competitive play and single player.
Quake II never made the same 'splash' that Quake 1 did, and everything that followed has been less and less popular?
I think the real issue is that Quake 1 'got lucky' with so many things in terms of it's crude physics. The quirky extra distance you'd get when you jumped off the lip of an incline, the sweet joy of a rocket jump (you could nearly eliminate the damage if you timed it perfectly) that hands you all the power-ups before your opponent can get to them, and the really basic set of weapons which left you with more time to play the game vs. learn it.
While TF/DOD is 'technically' a 'quake' based game (Steam Engine was based on the Quake Engine), it was the only FPS to really come close to the 'Quake' feel in the spew of games that followed, and it's followups had the same poor uptake as Q2 did compared to Q1.
BF1942 (using the Refractor 1 engine) was also very popular for it's "feel", and low n behold it spawned a mighty following of sequels that a lot of people say weren't as good as the original, even though the physics only got more accurate/realistic with each new release?
The opposite happened with Asheron's Call and AC2.. The original had terrible mechanics, graphics, and just an inferior 'game engine' all around. AC2 should have been a smash hit, but when AC1 players gave it a run they all had the same key issue: Not nearly enough game content. Which wasn't surprising because AC1 was packed with game content, including an in-game landscape that was unthinkably massive for that genre at that time.
I am still waiting for Turbine to announce that they have a new client that hooks into the old AC1 servers giving people who stayed with the game the graphics options of AC2 with the content of AC1 + all it's expansion packs. Sadly I doubt they ever will since they are very swamped with leads to build MMOs for all the major franchises...
Oh. Wow. Crap. I guess that I need to find my old CD key and revive my account?!