The experiences of my formative dungeon delving days of yore were classic Judges Guild. Tegel, Badabaskor, Dark Tower, City State, in general these are somewhat of a monster zoo, something in every room. Badabaskor has an overarching theme of the brigands, and Dark Tower of course has the twin towers to Set and Mitra interplay, but in general our group fought through room by room looking for loot. Fast forward 35 years and "Hey, it's been an hour and we haven't fought anything!" is still a somewhat common refrain.
That is not to say there are not thematic or non-violent interactions as part of developing stories, just that players mainly wanted to throw down some dice which in the early days most often meant fighting.
Here are some ideas I wanted to share about designing dungeons related to my experience with the idea that the number one function of dungeon scenarios is PLAYABILITY i.e. the dungeon's ability to assist the DM guiding a group of player characters through an environment in a way that is entertaining over multiple gaming sessions.
Judges Guild obliged with something to fight, or some challenge in every room and that's pretty much my philosophy as well. Perhaps some encounters may be silly enough to be essentially de minimis, or so overpoweringly destructive to be basically a player IQ test whether or not to confront the encounter, but things are always there.
Which is an interesting segue into game balance. I do not balance my encounters, but in general the lower number levels are the easier encounters which become progressively more deadly as the dungeon level number increases. In addition, however, I will purposefully will put some discongruent encounter on every level of the dungeon because it provides opportunities for characters to think beyond their fighting prowess and reminds them that dungeons are deadly. The reason all the loot hasn't been absconded with is on account of most of the would-be looters got killed.
Keeping the gamers on edge also help make the conclusion of any session more a natural and much needed respite than some sort of unfulfilling "oh look, it's midnight and we should stop." Parties should be concerned when they're running low on cure spells or offensive magic when there is not place to rest. Deeper in a dungeon your party should realize safe places to rest are much more important than treasure. Particularly when a party has scored a lot of loot, but is now contemplating what they must fight back through to escape the dungeon.
How do dungeon creatures eat? Interact with each other? Here I do try to group monsters somewhat thematically. For instance undead can sort of infect things around it, so you probably would find entire dungeon levels with undead dominated by them. Same thing on the "underworld" or "underdark"-connected levels. On these levels adventurers will likely find Underworld race strongholds surrounded by dangerous creatures these races enlist or nurture to guard adjacent caverns. I also tend to have water flowing through dungeons. It provides sustenance and also mixes up terrain for a combat sequence. (Also water attracts its own inhabitant nasties.)
Note that in my experience having a central theme being this Underworld tribe versus that Underworld tribe and the party needs to help X by doing Y is a recipe for disaster. You ABSOLUTELY DO NOT KNOW what your players will do. I have seen PCs, in an entire campaign devoted to ultimately destroy a heinous demon, at the penultimate moment, where to destroy an artifact found and used by the party to imprison said demon will forever slay it, then ask, "What do you suppose the demon would give me if I freed it?"
Another element I enjoyed as a DM was that Judges Guild provided a brief stat block typically with everything needed to run the encounter. This was not a terribly huge amount of information back in the OD&D times, but it honed my thinking that a DM should be able to run an encounter in general without having to flip pages or search through other books. That is probably the number one thing that comes out for me playtesting scenarios, "Oh, here is a place where I should have listed spells," or "this magic item really needs a description here for the monster to use it."
That is probably my main beef with skill points is that they increased the size of stat blocks such that it became difficult to write a nice, succinct encounter without lines and lines of stats, most of which is superfluous because never comes into play during the encounter.
Now, if I see a particular skill that ranks pretty high and seems integral to the operation of the encounter, I just add in the attribute some other way e.g. a +15 ranks in "Hide" for some kind of sneaking beastie will become a 75% Hide in Shadows.
Insummation (a single word that doesn't exist, but should):
1) Design dungeons around frequent encounters. Not exactly a random monster zoo, but keep the party moving and on their toes also with using the natural settings of the dungeon (pits, rivers, pools, lava, radiation, gas, etc.) to interact with a party during an encounter. Encounters through dungeon levels should be pronouncedly more challenging to the players with a variety of incongruent encounters interspersed.
2) Permit overall thematic aspects to arise organically i.e. provide the elements for roll paying various organized dungeon municipalities, but avoid making their conflicts the central theme of your game's stories. These are heroic stories and your adventurers are the leading characters. Let your party's actions provoke how much or how little organized sectarian conflicts become integrated with the story.
3) Make sure the DM has most if not all the information she needs to run each particular dungeon encounter. For my work, that means she should only be looking up spells and perhaps some magic items.