This is my take on things:

I believe that there is still a lot of potential for mappers to be creative and innovative with Vanilla Quake (standard monsters, standard weapons, but with fixed engine limits etc), and that there is a lot more gameplay potential to be explored. This potential may of course require trial and error and result in varying degrees of fun (equally I believe there is an issue with creating the "perfect" Quake gameplay by continual refinement. The pure fun level of a few maps in recent years shows that possibility). Obviously it's not going to break free from the "kill monster exit map" genre but I think mappers can break free from basic Id-style gameplay.

Consider various factors that can be used in maps:

Monsters that vary from very weak to fairly powerful.

Monsters that are good at close combat or good at ranged combat.

Monsters that are more or less susceptible to different weapons.

Monster in-fighting.

Weapons of varying degrees of strength and range-effectiveness.

Weapons of three different degrees of self-damage.

A high damage power-up.

An invisibility power-up.

An extra-health power-up.

An invincibility power-up.

A protection against slime power-up.

(All with time limits)

Fluids of varying degrees of player damage.

Traps of varying degrees of player damage.

A lack of falling damage.

Moving platforms, teleporters, crushers, spike shooters, explosive barrels, etc etc.

Then consider combining these factors and/or creating more themed, more focused gameplay. Here's a few ideas to be chucked around....some have been done, some haven't.

Horde gameplay with lots of monsters.

Maps with only the most powerful monsters and most powerful weapons.

Horde maps with hard monsters but continual power-ups.

Low-power maps with light monsters but light weapons.

Low-power maps with hard monsters, light weapons, but tactical use of power-ups.

Maps with biosuits and lots of slime.

Zombies, explosive barrels, and no explosive weapons.

Maps that specifically encourage in-fighting.

A scenario that relies on combining 666, LG, and water.

A scenario that relies on luring monsters into traps.

Gameplay involving the ROS and plenty of stealth.

Gameplay more focused on traps and jumps than purely on shooting.

Etc etc. Obviously just some raw ideas, obviously not all would work, obviously refinement needed. But just as something off the top of my head... 

Aim, dodge - thats it mostly. Some primitive resource management (ammo health). Straightforward navigation (which is better than e4`s dark mazes imho)
I dont see many maps that have interesting gameplay setups. Visual side evolved much more than the gameplay. Many maps are even worse than IDs original cause run&gun is all they have to offer. I might have missed some later releases, but nothing has improved since Damaul6 or Koohoo gamplay-wise. Just bigger areas/more monsters placed without much thought(which gets boring really, if its the only type of gamplay there is). I played Quake to death (felt that about 5 years ago) so Im no longer excited about simple fighting mechanic (which is good, but so old and wellknown).

Ofcourse there are more unexplored possibilities even w/o any mods. Need to stop relying on hordes and put more thought and creativty into gameplay design. But its hard. 

A map with 15 grunts and the shotgun only. With no health and no additional shells. Each of the grunts having a good chance to hit the player once if he isn't carefull/quick (an ambush, a small dark maze, grunt on a moving platform etc). The player should to be at low health and scared at the end of the map.
I also thought of making the monster placement semi-random for the replay value. This should be possible with quoth. 

what i like the most in a Quake map is exploracion and speed gameplay! 

Attack on Fort Ratsack and The Katagean Redoubt were great examples of gameplay. There was nothing flash-bang about the content and there didn't need to be, for me.

I didn't think 'this is crap, why isn't there a new boss monster' or 'why aren't I figuring out a series of button puzzles, boring' or even 'no normalmapping?'.

Its back to the million shades of brown analogy, I like the game as it is, extra stuff is a nice bonus but not necessary for me to enjoy playing it. 

I also thought of making the monster placement semi-random for the replay value. This should be possible with quoth. </>

You can set multiple teleport triggers on each monster entity, and randomize by using Fitzgibbon's patented shooter trigger randomizer, or make the teleporters trigger at different locations depending upon the route the player decides to take. 

Good post. It raises useful questions:

Some primitive resource management (ammo health).

Can that be improved? Can the player be challenged for resource management in more interesting ways? Perhaps given ammo-monster suitability...

Straightforward navigation (which is better than e4`s dark mazes imho)

Can that be improved too? I.e. navigation which is challenging, without being too maze-like...

Many maps are even worse than IDs original cause run&gun is all they have to offer.

Really?? How are Id's better then? I.e. what do they offer beyond run&gun?

Just bigger areas/more monsters placed without much thought(which gets boring really, if its the only type of gamplay there is).

Bigger areas and more monsters has been a general trend. I'm not sure if people are placing monsters without too much thought, I have noticed some cunning monster usage (one recent trend has been to force the player into Vore arenas with no cover, thus breaking the "dodge around a corner" anti-Vore-ball trend, and forcing continual running). But if that's another area to be improved, it's worth considering, i.e. maximising both monster effectiveness and monster fun.

Need to stop relying on hordes and put more thought and creativty into gameplay design. But its hard.

I agree with the horde thing, it was something that was tried, it offered a bit more fun and a different gameplay feel, but is not the only solution and can get boring (although I still think it could be pushed to amusing excess - 100s of dogs, the Quad, and RL....but as part of a quality map). And yes I agree it's probably hard, but it needs people to try. I go back to Ijed with Warpspasm's monstrous stamina-fest....he was prepared to give something a go... 

Ankh: Exactly!! That's the sort of ideas that are needed. It might not work so well first go, but those sort of gameplay themes are the ones to explore, I think...

Trinca: Exploration and speed gameplay. Even those simple concepts could encourage people to make stronger themed gameplay. I.e. maps that demand more exploration (subject so some ppls' dislike of E4 mazes of course ;)), or maps that force even faster gameplay....more relentless monster usage, or time limits maybe...

Ijed: I agree, both great maps with great gameplay. As mentioned elsewhere, I was impressed with just how striking Ratsack's secret areas were, even using Id textures and monsters!! I do think, going back to my first post, gameplay might not have changed in broad terms, but it's been refined in the details... 

Semi-random monster spawns: I've had this idea in my mind for quite some time now and was going to implement it in my current wip-map (multiple teleport triggers for some of the monsters).

The stealth/Ankh thing is similar to something I once discussed with inertia (maybe also posted about it before?). Player with reduced health (trigger_hurt damaging him to 10 or something upon startup) and lowered ammo, in a map of armor- (/damage-) hacked monsters, having to sneak through and discover ways of getting past them without arrousing too much attention. Problem is thsz standard Quake is not very flexible when it comes to stealth/enemy detection.

I have vague plans on doing a map with rudimentary adventure elements by using scripted sequences (npc mission, activating triggers, blah, firing counter), but in the end, it would still rely on the same old mechanics for the most part.

I've also been thinking for quite some about one of the suggestions Shambler made once (small, excessively detailed map, each monster as an event) - the problem is that people know by heart how to deal with each monster, e.g. if a grunt (or any other monster) appears, regardless of how cinematic it may be, a regular player isn't surprised at all or even scared and doesn't expect it to be special, simply because he has had encountered every monster in every situation before and knows how to deal with it. Increasing the monsters' health (randomly) might make it a little more interesting, but still... And since the recent? trend seems to be bigger=better (see the reviews - few monsters=too easy=downgrading element), creating fresh gameplay situations becomes even harder. 

is about big very concrete gestures while I think it's more about the subtle ways of controlling the players mind. Things like pacing, different kinds of contrast (open spaces vs. closed quarters, horde combat vs. lone monsters, all out action vs. moments of ill boding silence) in both architecture and entity use. 

I mean, challenging scenario for the player, is to put an easy to get quad just before you reach a rather snug area, and make it difficult to avoid receiving a rocket launcher in the area while being attacked. Such a trap can very from a mildly frustrating challenge to total evile depending upon how carefully you gauge the implementation.

Also, providing a difficult to get to walkway just above the jump range of a gang of hellspawns is another scenario that can lead to some tense drama because those buggers even after all these years can still be unpredictable.

The most satisfying part of game play design for me is finding ways to counter the player's expectations of how a common scenario should unfold. This is pretty much what bear is describing where it is mostly subtle things that generate interesting game play developed from tweaking the scenarios and keeping yourself open to possibilaties.

With ZerTM_HT, I originally had the exit teleporter in the little room behind the gold key door. I decided that was a bit boring and routine, and said to myself, there is a nice canal of lava running right underneath it, why don't we use it. 

Is very cool, especially when playtesting / replaying.

Lazarus Q2 supported it very well.

What's this random spawn method in id1, specifically "patented shooter trigger randomizer"? 

This is an old idea from another thread, but I'm not sure anyone has done it yet. Give the player a choice between two weapons and when the player picks one up, take the other away. I was implementing this along with route choices (circular connected areas you can enter from either direction) in a map I started last QExpo, but I haven't touched it in ages.