I agree with the idea of a Flashpoint reboot film. There was that scene in BvS that seemed to hint at Flash's time travel ability so maybe that was put in there to foreshadow it and give themselves the option.
As far as what could've/should've been done:
1. The origin films needed to be done before the big meet up. Man of Steel and Wonder Woman were good starts, but BvS happened way too early and Suicide Squad was just.....there. Should've given us either Flash or Aquaman's story before JL as well. Along with Cyborg, it's too many intros to try and make before getting to the heart of this story in JL. The Avengers characters were well established before the main film so the focus was on them trying to build chemistry and take on Loki as opposed to getting a background story on half the team.
2. They need to ease up on the CGI and add more realism to the world. This has been a problem for a while. Snyder seems adverse to using practical effects of any sort. I'm talking for both the characters and scenery. Cyborg would've been better if the actor were put into some sort of robotic looking costume as opposed to being CG for most of the film. Again, Wonder Woman did a great job of not overdoing the CG at least until the end. And by then, they had done such a great job establishing realism that the CG got a pass.
3. Every film seems to revolve around some sort of other worldly villain who's either from outer space or another dimension. It's okay to have a film with a more practical villain. For example, Iron Man didn't face any aliens until the first Avengers film, and we were able to see how that took a toll on him afterwards. Prior to that, he faced off against regular humans who happened to have extraordinary tech. It annoyed me that the Suicide Squad were going up against the Witch. It was too "out there" of a villain if that makes sense. It's like every movie has to have the huge, unstoppable monster that ends up being stopped Deus Ex Machina style. It's okay to have these characters go up against a regular human who becomes a villain like Vulture in Spiderman Homecoming.