After beating it again, Qud has two big problems for me.
1. It's too long and too linear, even with the randomly generated stuff, for a roguelike. Every playthrough feels roughly the same as a result. That makes dying extremely painful, and, due to the nature of some creatures, it can be difficult to learn from your mistakes as you won't see those creatures again for a long time. Bethesda Susa has a few of these (like those ice beast things that freeze you and then chomp you for 25 ticks of damage). The troll bosses on the way down aren't nearly as bad by comparison.
Roleplaying mode (respawns at checkpoints) feels much better since it saves you from skipping the redundant content (red rock, rust wells, six day stilt, salt desert xp farming, golgotha, etc.) you've already done a million times.
2. Every build ends up being roughly the same. Want to build a mutant axe murderer with multiple limbs? Awesome. Dismembering enemies is cool. After you get your melee skills up, though, you might as well learn tinkering and throw a few extra points in guns. Want to play as an esper and blow up people's heads? Want to shoot fire/ice rays? Want to focus on gas generation?
Those are all cool and different ways to play the game. But by mid game you will want to also use guns and tinkering because they're easy to get and very strong. Melee combat is especially hazardous as not letting enemies touch you in the late game is a major positive due to all the fucked up effects they will nail you with in melee range.
You could also just make a gun/tinker build right from the start and just never pick up melee/esper stuff. Even the terrifying punch truekin (punchkin) will prefer to eventually shoot stuff down because it's safer.
Where's the specialization? This kind of stuff ruins the power fantasy for me. Dungeon Crawl Stone Soup suffers from this too, where the best characters will want to eventually dabble in several areas as opposed to adhering to an archetype.
After all these years, ToME is still the best at delivering that experience. Zorbus is the only other recent roguelike I've played that scratches that similar itch while also being great in a more offbeat way.
Qud is fun but once the honeymoon phase wears off, all of its best parts - the exploration, experimentation, worldbuilding - aren't able to counterbalance your character becoming Goku with an assault rifle, running the same dungeons with fucked up, hard to navigate subterranean tiles, regardless of the class you originally picked. Yes, you can limit yourself to not using those skills, but you'd also be gimping yourself.