*Account for various combination of superpowers, or their lack. More than many other genres, you need to account for "Oh, the central conflict of this adventure is something I regularly resolve in my downtime." Murder mystery? Needs to deal with super-science, super-senses, necromancers, reanimators, and many more things. So, you'll need a pretty strong understanding of the underlying system, and what is and isn't possible, in order to make the adventure feasible.
*Absolutely no "Your powers don't work here!" areas. They're tedious and played-out. What are fun are "This villain or scenario has these effects, here are some interesting ways they interact with other power sources in the setting."
*Strongly-characterized NPCs. This, I think, is probably the most important part of any module; in my experience, PCs are far more likely to stick with a module and care about the outcome if the people they are interacting with are fun and interesting, and if they want to keep said people around after the adventure is over, you've got build-in sequel hooks.
*Good (but not overwhelming) ties to the existing setting / metaplot. Most games will at least gesture in the direction of the existing setting, so having things that tie into that
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One of the favorite extended modules that I ran for my group was for Mutants and Masterminds 2E, called Time of Vengeance. It's a fun and involved adventure featuring a crises themed around the Ten Plagues of Egypt. One of the things that it did well was that it let me pick out which of the plagues were going to be fully-realized encounters, and which were going to, as a result of player choices, be mere side-notes or supplements. (For example, the plague avatars who used insects or frogs were very ineffective against the ghost PC, and so those encounters mostly instead because showcases of the underlying baddie, and what happened to the avatars when they didn't fulfill their role.)
There were ten separate villains, each with their own motivation, and a strong selection of side characters; one of my PCs ended up picking up one of the de-villainified plague avatars as her own kid sidekick based on his literal scenery-chewing (he was Locusts), and the final villain's story and history was both key to defeating her in the non-violent path, and doled out surprisingly well over the course of the module. And because her backstory tied interestingly to decades-old history of the Freedom League (the setting's JLA/Avengers equivalent), the group was motivated to learn about her not just to resolve the current situation, but to learn more about them. M&MM is a specific, simulationist-over-narrativist rules set, which is not the most popular these days, but if you're in a similar ruleset or setting, I'd recommend seeing if you can score a copy to look it over.