There is the stuff I mentioned that seems to fit the OP - intrigue, scarcity of resources (especially water), etc. - but you can probably find that anywhere. Also psionic powers.
IIRC there were other things... Like the dragons that get warped by power, similar to the God Emperor of Dune (haven't read the book, just know about it).
It is the best setting I can think of for "fantasy RPG Dune". There might be others, I don't know.
EDIT: also this:
Darksun is nothing like Dune other than they're set in desert-settings. Darksun is post-apocalyptic dark-ages sword-and-sorcery. Sure they have surface level similarities - but those conceits are largely superficial. Dune is feudal and deeply political and factionalized with a ginormous amount of religious mysticism at the core asking ginormous questions about the fundamental natures of people. Heady stuff for an RPG to be sure - which I'm less concerned with. But they're elements that greatly informs the setting.
It's one of the things I generally don't like about most D&D games I see when it comes to spellcasters, and divine-spellcasters in particular: a reductionist view of how of those forces, and those that wield them are completely absent from the setting's own assumptions. Clerics are reduced to just "the party healer", casters are "glass-cannons" and the context of those individuals as somehow "normal professions".
Dune takes all these things in their respective manner into account. In a Fantasy-version of Dune, the same tact with some twists would have to be established as well to establish why the world is as it is.
1) Being from the Sisterhood/Counters/Guild would have immediate implicit assumptions tied to it. Basically their factions have deep control over their activities. One of the conceits of Dune though it's rarely an issue - is that depending on how high-up the food chain within these respective factions you are, your abilities are predicated on obedience to your faction which they control via the various addictions you've acquired to maximize those abilities.
2) The world has to reflect the *need* for these beings to exist. The very abilities of these factions are the commodities they alone control. The Sisterhood are the ultimate in negotiations and even to some degree in spying. The Counters are masters of whatever skills they've trained in to super-human degrees, spies, assassins, strategy, logistics etc. Guildsmen are commodity controllers of production and the ability to acquire things necessary for the other factions to even survive. This would mean the Faction rules in play would have to account for these things. So being in bad-standing could cost you your life.
One good direct connection you made is the Dragon Lords <> God Emperor. Structurally they kind of inhabit the same space. But for the purposes of a Dune Fantasy RPG that would be way down the line. The God Emperor doesn't come to fruition until the end of the second book in the series and there's a LOT that could be done before that.