I think resisting "easier is just fewer monsters" design is the right way to go. There should be fewer monsters, just not many fewer, because too few is just plain boring. We're all Quake Experts after 20 years of this, so I think anyone playing custom maps on Easy in 2018 is doing so because they're doing it on a lunch break or a stolen evening away from the kids, and not because they can't handle more than one fiend at a time. Maybe we should think of it more as 'higher investment.' Besides, Quake gives you tons of unappreciated variables that you can tweak by skill, both obvious and subtle.

- Armor makes Quake significantly easier. More reds and yellows, more often, effectively extends the player's survivability in a given fight by hundreds of HP. More Greens, or stretches without armor at all, shrink the until-death buffer to little more than the player's current health. If you do want to keep the same monster loadout on all three skills, give the Easy player several Red and Yellow armors and the Hard player only one or two Greens. They'll feel like completely different games.

- Adding a vote for weapon pickups coming earlier or later. On Easy, the next big weapon might come before the next big encounter so the player can kick ass with it, on Medium it might be placed within it so the player has to engage to grab it, and on Hard it might only come as a reward after beating the fight entirely without it.

- Greater monster variety leads to more ways the player can be attacked at any one time, requiring juggling more variables to avoid damage and find the safe place to be standing at any given millisecond. A shambler and a vore together are harder to handle than a pair of either. Variety also raises the chances of infighting, however.

- The angles that enemies are presented from makes a difference. In front of the player is easier, flanking is harder, behind is bordering on unfair depending on circumstances. Below the player is a turkey shoot, eye level is straightforward, and monsters up high have a distinct advantage.

- Quantity of resources matters, of course. Bigger medkit pools clearly make the game easier, plentiful rockets can be splashed around while rare ones are only for emergencies, etc. Nail weapon DPS is higher than SG/SSG DPS and so on.

- Frequency of resources matters too. A steady drip lets the player feel secure, but isolated bursts create situations where the player has to stretch himself to get to the next 'island'. Depending on where he makes his errors, he might have to stretch pretty hard (eg those 'quicksave with 5 health left' or 'shambler axe dance or bust' moments). Feast-or-famine item placement can induce mild stockholm syndrome, leading to more positive reviews :)

- Unless you're using a lot of Enforcers, maybe provide all players an early Lightning Gun and simply vary the cells provided, as a way of dealing more or fewer 'get out of jail free' cards.

- Don't forget that the difficulty spawnflags are present on every entity. If you're using monster closets, vary the locations of the ambush triggers. Have the Hard ambushes happen when the player is in the worst possible position, and give them a leg up or more warning on easier skills (or even leave the closet open on Easy so there's no surprise at all). You might even duplicate the doors so you can set different 'speed' keys per skill, so the harder ambushes are an instant pants shitting and the easier ones are more like a countdown until the monsters come out, complete with early warning aggro sounds. Doors can be temporarily barred behind the player on hard skills while he is free to retreat from a fight on easier ones. Falling into a pit can be a mild backtracking inconvenience on easy skills but death by spikes on harder ones. How much room is there between nail shooters in this hallway? With careful use of triggerable lights and skill-specific trigger_relays, you can even use light and darkness against the player differently.

Getting crafty with what you change between difficulty levels can give you ideas for entire encounters, although don't rely on that too much for interest, because any given player is probably only going to experience one such permutation and thus won't realize the need to appreciate how different it is from any others. 

Great suggestions above. I may steal this and create a "gameplay" video based on it and a few other posts. This is an area I struggle with and just two or three of these suggestions would have have a big impact on any map. I know some players hate "back spawning" monsters but I think if you use them sparingly as an easy task after a more challenging encounter they can be effective. 

Here's a method I've been using. It's really rough, and time consuming without a custom progs to do it for you, but it can be a helpful way to ground your estimates.

A box of:
25 or 50 nails = 225 or 450 damage
20 or 40 shells = 440/880 dmg
6 or 12 cells = 180/360 dmg

6/12 rockets are harder to judge because of 1) splash damage and 2) zombies, but let's say every rocket is 180dmg, for 1080/2160 dmg per box.

Total all the ammo you provide in the map (add 25 shells for the starter ammo, add 2 rockets per ogre and 5 shells per grunt and so on), and that's the max amount of hit point damage you are giving the player to deal. Total the starting health of all the monsters, and compare the two numbers.

Researching id maps and popular custom maps reveals an average 'custom' of about ~3:1 on Easy, ~2.2.:1 on Medium, and ~1.7:1 on Hard. the id maps are generally above that curve (4/3/2:1), and custom maps tend to fall below it(2.5/2.0/1.5:1).

Careful cheapskate shot-counters can finish a map with a ratio of about 1.3:1 ammo DP:monster HP, but most players will have to resort to the axe at some point and will complain of shortage. RPGSP1, which was greeted by universal reviews of "good but I ran out of ammo at the end" still had a ratio on skill 2 of 1.4:1 DP:HP.

There are lots of outliers to these curves, though, because so much of it comes down to how the level design enables the player to *use* the weapons, as well as exploit infighting, choke points, etc. Do rockets get spent one at a time on individual zombies or can they be used to gib crowds of knights for maximum ROI? or are they useless against herds of shamblers?

It also matters when the player gets the ammo. Ammo the player doesn't pick up or can't use is effectively not present in the map at all. Does it come too late to be used when it was really needed? does it come too early and get skipped? or partially wasted when picked up by a player who's already nearly maxed and getting too much at the wrong times? How much of that ammo is in secret areas? 

20/40 shells * 24dmg/shell = 480/960 DP per box 

also quad damage placement 

Right there with you buddy. I once made a mod that outputs my health, shells, nails, etc to the console once per minute. Then I graphed it for my favorite levels. Made sort of an S type curve and tends to plateau with plentiful supplies of ammo towards the end but health still only hovered around 40 to 75. 

I always come back to this: to heck with the numbers, make it fun. 

I cannot caveat enough that such measurements are of little exact use. It's good for ballparking it and discovering "oh shit I'm way off" and don't trust it more than that.