As much fun as it would be to dive in to shit-kicking Marvel's dumbfuck decisions, I'll try to answer your question OP.
At the risk of sounding like a disgusting little shill, I have been working on my own comic universe as a sort of pet project. Its meant to be more "pulpy" than a modern superhero comic, similar more to Hellboy/Lobster Johnson comics than Spider-Man.
So first thing I did was establish "commandments" on what the theme of the world was. So for me it was:
1. Set in an alternate Earth around the 1920-30s. Many facets are similar but key historical facts are changed to justify the new world here and there. The point of this is to avoid going anywhere near "real world issues". No awareness comics, no agenda drivel, no "My ward's a junkie!?". Just stories and the characters that drive them. I also drew up a bunch of shit on what technology people are using and the limits of it even when considering mad scientist shenanigans (like computers), but I'll contain the autism.
2. I drew up a sort of key staging ground for most of the stories: Imperius: The City of Wonders.(still working on the name, pls no bully) A sort of combination Gotham/Metropolis/New York City that almost has mystical quality. (Like an Art Deco Valhalla) City Limits are kept vague, as their is always some new unexplored neighborhood or alleyway to have stories. The city isn't meant be looked at as a whole, but as a container for the greasy diners, high rise apartments, and hidden corner stores that all the protagonists will live in and experience.
3. The setting takes place as a backdrop for some unexplained, never-ending great war happening across the sea. With the adversary never quite explained, only given a vague title like "The Homeland". Now, the whole war effort is meant to be suitably vague and mysterious, as its not meant to be a center focus but as a means to introduce new plot points. Foreign spies, deadly weapons, military coups, political intrigue, etc. This may be just because I have a thing for Noir settings but eh.
4. No Superhero Alliances or literal hordes of costumed vigilantes. Superman-like characters when not in their own independent settings only serve to trivialize street-level heroes with constant cosmic level threats to handle. More so, giant leagues of superheroes invalidate the threat an individual superhero might face because why the hell wouldn't he call for backup? So what I want is to keep most characters relatively mundane so as to lend a certain seriousness to their varied adventures.
5. Each protagonist would have a mini-Bible to establish character personality and story continuity. Writers should approach established characters with the same reverence Don Rosa had for Carl Bark's Scrooge.
6. If a character can't stand on its own in an independent story without constant "guest heroes", it doesn't get to exist. Something like Batman Beyond would be great because even though Batman is already established and Bruce Wayne still a central character, Terry has his own personality and struggles, and doesn't rely on being the new Batman to be good, he just is.
I have no experience with this sort of thing, but its what I've come up with. Beyond this all I have is character concepts, like a animal-talking hobo-sage or a shovel-wielding Irishman who fights necromancers and ghosts. But I don't wanna bore.