You all have heard this explanation before, on why a large demographic rather wants to read manga than comics: Because they are individual ongoing stories instead of several dozen smaller ones all written by several different people and sometimes even rebooted and retconned with occasional one-shot stories mixed inbetween that might not even be canon.(and nowadays most comics tie in together with other crossovers, making it even more of a mess to get into)

The question is though, if one were to assume Batman, Superman, Spiderman, X-men etc. didn't exist as they do now and instead someone today would come up with a story of one of them in a publishing style similar to manga, what kind of plotline would they have? How would you handle them?

Even though many have had longer story lines before, almost none were intended from the beginning or work together from a narrative standpoint.
Like, What does a guy dressed as a bat have to do with a Joker? While their personalities do make a good match as protagonist and antagonist, their themes do not work at all. Or a spider and a goblin(or alien goo; octopus; etc.)
However a good example is pic related. Brainiac and Superman all tie in together in one big ongoing plot, Superman TAS made it work quite well.

So if you had to reboot a cape comic and had to rewrite it from the beginning, what kind of plot line do you think would work to make it a great stand alone ongoing story?