I see what you mean, but I'd like to think that Joss Whedon wouldn't have taken it on if he didn't think it would be good.
Plus there is precedent for good results from these kinds of major reshoots. The major recent example is Rogue One which had extensive reshoots and an almost entirely different ending than it originally had.
Whedon being involved makes me feel much better about the potential quality of the film. Having said that, something about his interaction with Marvel went wrong on Age of Ultron, and that doesn't inspire me to believe he's necessarily a good clean-up guy. We'll see, but Whedon is better than Snyder, so it's generally a net positive.
I absolutely LOVE 300 and I liked Man of Steel, but Snyder is all glitz, shaky on substance. As long as a film looks good he doesn't seem to really know if it's actually an overall enjoyable, relatable film or not.