The question is, what would make the Batman movie a better launching pad than Justice League? JL should be a good movie with a solid script, regardless of what happens with BvS. They should have people from Warner Bros and DC going over the script to make sure that Snyder isn't going crazy, and they should be showing that script to the people making any of the related movies, just so they can make sure that everyone is on the same page. Snyder isn't working in a bubble here. He is part of a bigger machine.
Well it's building on what works and fixing what doesn't. If you'll allow me to speculate, let's say that the Hitfix rumors are correct. Batman works, Lex works, but the rest of the movie falls flat. That means that Wonder Woman doesn't impress, and something about Superman doesn't work. And to continue to play devil's advocate, let's say that Superman spends the whole time being angry and doesn't do anything heroic. And maybe they don't like how dark (lighting, not tone) the whole movie is.
WB looks at the script for Justice League, and they look at what's in there. (speculating again). Batman's in it fine, but Lex is either barely in it or not in it at all. So maybe they rework it so that Lex plays a bigger part. Wonder Woman didn't work in BvS, but her movie is coming out so they sorta have to run with whatever is established in that movie. Perhaps they could make some slight alterations in her character. But with Superman, there's tons they could do. Maybe you open the movie with a fun action scene that spotlights the kind of Superman that people want (I'll get to this in a second) - sorta like how Singer would've re-written Superman Returns to open with the plane crash. Maybe you alter his character to make him a little happier - a little less moody. And whether or not you keep Snyder, maybe you tell him to cut back on the sepia/gray colors and throw in some color.
That's all they'd need to do. And if you release Batman before Justice League, you give yourself time to fine-tune these kinds of things.
And it's not like they can't do stuff like that. If you have Affleck's Batman, and that's what works, then you use that and build on it. Make no mistake, the MCU has succeeded because of Downey's Tony Stark character. People liked Iron Man, but look at the rest of the phase one. Incredible Hulk bombed so much that it's barely canon. Thor is no one's favorite movie. Captain America: the First Avenger is a glorified trailer. Heck, Iron Man 2 is a mess, and it's the second-best pre-Avengers movie.
Avengers worked because it a) had Iron Man and b) made the rest of the characters work, altering them if-necessary. That's why no one gives a damn about a Hulk solo film, but they go nuts for every Hulk scene in the Avengers.
So you apply that plan to DC. If Superman doesn't work, make him work in some other way. And I don't necessarily think that it's Donner. I think pretty much every DCAU movie/show gets Superman right. He's a great leader, he's tough, but he's fatherly/brotherly. He lightens things up a bit when it's not time to be serious. I think the problem with MoS Superman (that seems to be carried over into BvS) is that he doesn't really have fun being Superman at any point. Now the second Zod shows up, the guy should be all business. But it's just weird that the two most fun scenes in Man of Steel both happen *after* the Battle of Metropolis, literally the only time in the movie that fun shouldn't be happening (again, IMO).
Max Landis gave my favorite description of Superman in a video he did. He said "instead of absolute power corruption (Clark) absolutely, absolute power has absolved him from fear and greed and hate and all the weaknesses that stem from human insecurity." And I think that's brilliant, and it turns all the "boring" parts about Superman into really fun, creative things. I can imagine a scene in a Justice League movie where they're hanging around a situation room table talking about why they became superheroes. And Barry talks about how his mom was murdered and his dad was imprisoned and how that turned him to the law. And Diana talks about how it's her legacy to protect mankind. And Arthur says he wants to do right by his people. And maybe Bruce mentions his parents or whatever. But Superman looks around and is a little confused - he's a superhero because it's the right thing to do. And everyone sorta laughs at the innocence of that, but it shows Clark as this guy who has all the super powers but the strongest is his belief in mankind.
And while I think Man of Steel actually captured a lot of the things right about Clark, I don't think it captured his super-optimism. I don't think it captured his light-heartedness or his fun side. And I think, more than just cramming Superman into the Nolanverse, I think that was my biggest issue.