Note: since I don't play much of WRPG's, I'm gonna be exclusively talking about Japanese RPG's and DRPG's
Are you asking for good dungeons in RPGs? Or good DRPGs? Because both are different questions. In general, I've found DRPG's to have such thoughtful dungeon design that the exploration feels as important as the random encounters. DRPG's also feel more focused on resource management, since you're always considering whether you have the resources to get out of a dungeon too. Not to say JRPG's don't have resource management, some do. But most JRPG's haven't made me thinking about it to the level of DRPG's.
On the specific questions:
Random encounters: I can deal with any encounter system... so long as the battles are done quickly. I'm not saying the game should be a breeze (I absolutely expect boss battles to present a challenge) but battles shouldn't be me spending 10 seconds deciding what to do and then me waiting 50 seconds waiting for it to play out on screen. Make the battle animations quick and snappy. This really makes a difference. Even games with good battle systems get dragged down by long attack animations.
Now, while I just said I'm okay with any encounter system. I think more games just need to straight up copy the encounter system from
Labyrinth of Touhou 2. LoT2's encounter system is genius. It gives you a visible encounter rate bar that goes from 0 to 100%. Every step makes it randomly go up by a small value and as you might expect, the more steps you take = the higher chance of you running into a fight. This system is so good because you're never in fear of taking 3 or 4 steps before immediately running into another battle. And if you ever need to grind, there's a solution for that too: there's a button that lets you instantly set the bar to 200%.
(You can see the encounter rate bar on the top right, under the mini-map)
It's a good random encounter system that's, honestly, kind of wasted in LoT2 since the game is a DRPG with maze like floor layouts. Now in a regular JRPG, where dungeons are rather streamlined, it'd work way better since you'd have the dynamic of "sticking to the main path and having less enemies to fight" vs "going for optional goodies that will almost definitely make me fight more enemies"
Seriously, more games need to steal this mechanic. It's a much better way of doing random encounters than most JRPG's.
Extra Stuff: I don't tend to care about optional stuff, but if you're going to make me farm materials, there should be some multiplier/bonus that help makes grinding less annoying. To bring up Labyrinth of Touhou 2 again, that game has both: systems that reward you for consecutive fights (e.g. you get a multiplier the more fights you complete in a dungeon; it also has a challenge system letting you get rare loot with a 100% drop rate if you do a boss at a specific challenge level) and characters that help with the tedium of grinding (e.g. some characters have passives that increase rewards after battle, other characters have skills that work like "if you kill this enemy with this skill, you multiply the exp/gold/drop rate")
Good Dungeons: I'm gonna be honest, I don't like most dungeons in RPG's. I'm struggling to think of any dungeons I actually like; most I've run into are boring or straight up bad. I dunno if OP is doing research because they're making a game but if they are: please add maps that actually give you information. I recently played two RPGs with awful in-game maps (one was Okage: Shadow King which, doesn't explain landmarks, and is functionally useless for any dungeons with maze-like layouts) and having maps that don't work is honestly worse than no maps at all. Make sure your maps are actually useful.
The best comparison I can come up with is strategy RPGs where you essentially never fight the same battle twice. I just don't know how those kinds of games work with dungeons.
The Arc the Lad series is an SRPG with dungeons. In Arc 1 there is only 1 dungeon and enemies respawn immediately after leaving a floor. Yes, that means to get out, you have to fight your way through all the floors you've cleared. The game also does the usual SRPG thing of "battles are replayable for grinding reasons" but there's technically only 1 proper dungeon. Arc 2, which is a proper JRPG just with an SRPG combat system, has fixed encounters in dungeons. These also always respawn (unless it's a story important dungeon that disappears once it's completed). I have never played Arc 3, but Arc 4, which is a 3D SRPG, just straight up has random encounters
