A new Justice League movie hasn't really been announced-- Zack Snyder just dropped a comment that if they do a Justice League movie, he thinks it will be separate from The Dark Knight and The Man of Steel. We don't know what will actually go down when they finally do make a Justice League movie though, because it hasn't even been announced.
While there are cons as well as the pros to doing a movie that teams up actors from multiple DC Superhero franchises, to paraphrase what one savvy poster said in the comments for the latest article: we don't need two James Bonds in the movies at the same time, so why do we need to two Batmen or two Supermen? It's not like putting Henry Cavill, Christian Bale, and Ryan Reynolds in a Justice League movie is going to ruin the separate Superman, Batman, and Green Lantern franchises.
Being a self-contained story does not mean that they have to sever any possible continuity with the solo films-- in fact, from a writing standpoint, it would be HARDER to deliberately establish that this is a different Batman and Superman from the solo films without smacking the audience over the head with trivial inconsistencies in their backstories ("Hey Batman, remember that time when you weren't trained by Ra's Al Ghul?") than it would be to just use the backstories they already established in the solo movies.
The hard part is not in the writing of such a movie, but in the money and the egos, which is what Marvel has been learning the hard way in regards to the Avengers film. Marvel owns a fair share of the problems they've had in getting the Avengers movie off the ground, but it's not like anything like Avengers has been done before, and there's going to be growing pains.
When you have a group of established talent from big movies it's not always easy to keep all of them happy, and unfortunately Marvel tends not to call people back if they're asking for a lot of money or creative influence. Terrance Howard got dropped from Iron Man 2 because Marvel decided that they accidentally paid him too much for the first film, Edward Norton got the boot from Avengers because he didn't like sucking up to Kevin Fage, and Jon Favraeu left Iron Man 3 because he was getting fed up with all cross-franchise references that Marvel was pressuring him to include.
I think what DC needs to do is come up with a good compromise: they promise not force the directors of the solo movies to include any cross-franchise references in the movies they make, as long as they don't do anything stupid like stating outright that Superman is only a comic character in a Batman movie or something like that. Meanwhile, Warner Bros. makes the Justice League movie as a self-contained story that draws on the continuity of the solo movies as its backstory, and has a plot where the League must unite against a common enemy, and at the end they go their separate ways.
The whole "Reed Richards is useless" issue doesn't have to come up if as long as Warner Bros. limits the scope of the DC movie-verse and recognizes what each hero is for. It's not like Batman is going to go to Metropolis to try and fight a giant robot or alien or whatever. Hal Jordan spends most of his mask-time in space busting interplanetary bad guys, and Superman can't exactly be in multiple places at once. Continuity becomes a problem in comic books, where you have hundreds of costumed characters that the editorial staff has no hope of keeping track of consistently, but in a movie universe where you have 5-7 heroes it's not as big of a deal. The world is a pretty darned big place, after all, and if we had superheroes in real life I doubt they'd run into each other all that often if they are all in different cities around the world.
