I like that Johns and co. made changes to GL so that Waller could be included, as well as Parallax, Krona etc. because, even though the movie doesn't have to reference other heroes or setup a JL movie, these characters are part of the larger DC universe anyway, and can be used for other future solo movies or a teamup movie. The same way the comics can use these characters for their individual stories, while they also have played a part in other character's stories. But if recurring characters like Waller are used within the individual stories, it doesn't mean it has to set up a particular story for the JLA movie, since that hasn't been figured out yet. That's when it starts taking away from the solo movie's story, trying to be all about setting up a teamup movie. But if it serves the story, I wouldn't mind seeing something like Checkmate or S.T.A.R. Labs used in more than one movie.
I still believe a JLA movie is a possibility down the line. When solo movies are established, when they see how WW has done on TV, when they finally decide if making an Aquaman movie is possible. But obviously, what Johns and co. are stressing right now is that it is not a priority.