Regarding the "negative perceptions," we should perhaps remember that a good chunk of that comes from the modern expectation for total transparency regarding behind-the-scenes stuff and the tendency of today's entertainment media to track every project from conception to finalization, which can give the impression that any given project is "troubled" at various stages in its development.
Making movies and TV shows is a messy process. Cast changes, personnel changes, script changes, reshoots . . . those aren't necessarily signs of trouble, but just evidence of a work-in-progress.
Heck, look at Trek's own history:
1965: "Ohmigod, this STAR TREK project sounds like a mess. NBC rejected the first pilot altogether. Jeff Hunter has bailed on the project, probably for the sake of his career. They fired pretty much the entire original cast, including Roddenberry's girlfriend, and just kept the guy with the ears. Now they're starting all over again with a whole new script and star. Sounds like a train wreck to me."
1978: "What the heck is going on with this new Star Trek movie? First it's supposed to be a feature film, then it's the premiere of a new TV series, and now it's a feature film again. And they were going to replace Spock with a new Vulcan, but now maybe they're not? And they're rewriting the script daily, even as they're filming it, and rushing to make an impossible deadline that won't even allow for any test screenings. And I hear that the original special-effects team didn't work out and needed to be replaced by a whole new team at the last minute. This is a disaster in the making that's going to mean the end of STAR TREK."
See what I mean?