I'm in two minds on the cutscene usage. On the one hand, I prefer to remain in control, and more importantly, in character, rather than get a weird third-person cutscene right before the action. The way it was handled in some games (including D3) took me out of the game, rather than aid immersion. On the other hand, where used properly such effects do tend to add to the dramatic effect. I'm not so sure I think the FPS genre needs that kind of thing, or whether it can use it without making it a gimmick. However, I do appreciate the gaming industrys attempts, succesful or not, to bring gaming to a kind of maturity on par with the cinema -- so long as there will be at least some games that stick to the old set-up..

I prefer HL(2)-style dramatics-, immersion-, and cinematographical aids: they set the mood, but keep you in the game.

Wow, I've missed out on quite a bit of discussion so far...

I too feel the DOOM 3 engine would have been perfect for a Quake 1 sequel.  I need to reinstall DOOM 3 so I can check out the Shambler's Castle mod.

I personally liked the inclusion of the PDA in DOOM 3.  I will concede that some of the audio logs ran long though.  It would have been nice to be able to move around while listening to one.

I also liked the inclusion of NPC's in DOOM 3.  The sentry guns were really your only friend in that game.  Everything else was trying to kill you.  Quake 4 was a little better but once you became "stroggified," you were on your own again.

As for the color palette of a game, I prefer vibrant and contrasting colors.  Quake 2 came out when colored lighting was still a relatively new thing.  As such, it had all sorts of crazy color combinations and I loved it.

DOOM 1 & DOOM 2 were about action first and horror second.  DOOM 3 was a let down for me because it focused far too much on the horror element rather than the action.  Its expansion, Resurrection of Evil, did a far better job of balancing the two.

The sewer portion of RoE is a great example of this.  You had a long narrow corridor populated by many enemies, a chain-gun full of ammo, and a desperate need to get to the other side.  The helmet that shielded you from the poisonous air also enhanced the mood by muffling all of the noise around you so that you could only hear the rapport of your bullets and the dying screams of your enemies. 

Returning to the Delta lab was also a wonderful mix of horror and action.  The entire section phased in and out of Hell.  You'd be in an empty corridor one moment and then surrounded by damned souls the next.

Painkiller is also in the vein of DOOM although it plays more like Quake 1 in terms of movement.

I like ambient noise, but I'm not a big fan of ambient music.  (I hate most of Quake 1's soundtrack.)  I also like triggered music, but I don't like it when it's only triggered by being in combat.

I personally think Raven did an acceptable job at recreating the Quake 2 universe in Quake 4.  The architecture was decidedly Stroggish sans the crazy colored lighting.  The character designs for the Strogg were generally different but still adequately disturbing.  I also thought the inclusion of squad-mates was appropriate given that you're fighting a war and that you weren't the only survivor this time.

As for the arsenal, well I think they were going for a mixture of weapons past and present.  I didn't mind the choice of weaponry so much as the choice of sounds that accompanied them.  The Quake 4 nail gun produces one of the most obnoxious sounds I've ever heard.  The fact that you come to rely on the upgraded form of the nail gun later on in the game just makes it worse.  *CHINK* *CHINK* *CHINK*

Oh and you also have to give Quake 4 props for the drop scene.  That screamed nostalgia.  (It was one of the few instances where a game made me shout out in glee.)

In regards to why the setting and story changed between Quake 1 and Quake 2...

I remember reading something about that in one of the interviews of John Carmack during Quakecon 2007.  He said something to the effect of that they wanted to call Quake 2 something else but every name they tried was already taken so they just stuck with Quake since they had the rights to it.

I too miss secret areas.  Puzzles are too often used now to pad out a game's length.

As for cut-scenes, I prefer third person but I don't mind first person when it makes sense.  I don't want to feel like a camera attached to a pair of disembodied arms.

In regards to DOOM's 3 cutscenes, I too feel that the monster introduction scenes were overused.  The only two I really enjoyed were the pinky demon and the cyber-demon.  I liked the pinky demon just because it filled you with a sense of dread about what the beast could do to you if it ever got close enough.  The cyber-demon scene just made you feel horrifically underpowered and insignificant (which is why the actual battle is so ridiculously anti-climatic.)

And I think that's everything I wanted to respond to... :p

It was. Just click away the PDA, and the log keeps running.
In D3 (as opposed to Bioshock) you would actually be unlikely to run into anything while listening to the log, provided you don't just run to the next fight-zone.