JPL said:
Absoultely --- "they take it at some known point, strip out everything they don't like, and run what's left with the understanding that nothing that happens in the comic books matters any more." Every group that plays in some sort of established ongoing fictional universe --- Marvel or Trek or Buffy --- runs a sort of "parallel universe" version of the setting, ignoring or contradicting new events or even established continuity as they see fit, and adding new elements [the PCs and their adventures, for starters].
I dunno...maybe I'm assuming that my own personal preferences are widely shared. To me, the best option is to set the action in a relatively isolated area of the established world --- Marvel LA, for example. That way, I can bring in the Wrecking Crew or SHIELD or Rocket Raccoon if I need to, but the PCs are still the biggest heroes in town, instead of cleaning up when the Avengers, the FF, the X-Men, the New Warriors, Wolfpack, etc. are all otherwise occupied.
I'll agree with this, yes, current Marvel and DC continuities are mixed all up, but most people who are interested at all in superhero games know at least some version of those settings, and the details of continuity might change, but the basic concepts stay the same. They know about Gotham City or Marvel NYC, they know who S.H.I.E.L.D. is and what Star Labs is, they know to look for a copy of the Daily Bugle or Daily Planet for their morning newspaper. Even somebody who hasn't read a comic before, but has watched the Batman, Superman & Justice League animated series knows enough about the DCU to roleplay in it, for example (especially if the gaming group decides to use that version of the universe).
I don't read much in the way of comics, but from movies, TV shows and video games that I have a mental image of both Marvel and DC, much like a typical D&D fan has a view of Typical D&D Setting they know of but aren't a big fan of. You don't have to be an expert on the lore of the Realms to play in the Realms, you don't have to be a big expert on the continuity of DC or Marvel to play in those worlds.
I'll also agree that they can just set the game in another city (or a disused part of an existing city), to ensure that the PC's are the stars, and while the Justice League (or the Avengers, or whoever) might be out there, the PC's are the ones who are on-the-spot right now and have to be heroic to save the day (after all, for the zillion super-teams in Marvel, they all seem to always have stuff to do
).
The details of continuity might change, but they do that with any two fans views of a licensed product (with the convoluted and contradictory canon of Star Trek, a Trek RPG has the exact same problems, and with various views and opinions on Star Wars, that happens a lot too). At the beginning of the campaign, you just have to make sure that everybody is on the same page, and willing to play along with the GM. If there is any conflict, well, comics generally created retcons, so it's even in-genre to retcon things away in the game.
The MU and DCU are what most casual superhero fans know well, and creating some elaborate new setting as a thinly veiled take-off or based on a relatively obscure comic book isn't really what is needed. Especially given the way WotC works with d20 Modern based products, providing toolkits and letting the DM's build what they want with them (even the Urban Arcana "Campaign Setting" was just a high-magic toolkit for the game with a few setting elements thrown in, and some stuff that seemed like it was cut from the core book for space like the equipment chapter).
Now, if d20 Superheroes is added to the SRD, and somebody wants to take a chance on such a product, more power to them and I wish them well, but a niche product that small I really can't see it being WotC's style. Now, if WotC somehow bought the license to Marvel or DC settings that changes everything, a d20 based licensed Marvel or DC RPG with the backing of WotC would almost certainly be a huge hit.