3. The Story Is Restricted
When you start a film from scratch or make a sequel or spin-off, apart from your starting point, you can go in whatever direction you feel works. You can alter and kill off major characters at your whim, vastly expand the story you're telling, and even take it in a completely new direction if you want. But if you're making a prequel, doing this is considerably harder. In a prequel (at least a direct one), the story has to tie into your source material in some way. Even if the connections are incredibly tenuous like in Prometheus, there has to be something bridging the gap between the original film(s) and its prequel. Which pushes you into a corner in terms of story because you have to make the new story fit in with the original one to some degree, taking away a lot of the freedom you would have in a sequel or spin-off. Imagine if, against all logic and reason, Warner Bros decided to make a Harry Potter prequel about Voldemort's early life and rise to power, culminating in the First Wizarding War. Before you even draw up a story outline, the whole story has been more or less completely told in the books and films from a year before Voldemort's birth right up until his first defeat, which would leave very little space for original plot developments. A hypothetical Harry Potter prequel isn't the best example here since Voldmort's story is told to us in such unusually specific detail but the point still stands. As far as story goes, a more direct prequel is severely limited in what can be achieved since it has to be kept on track with its source material in order for the larger story to be coherent. Which will only serve to harm the film because it means there is a list of required elements that have to be fulfilled in order for the full story to make sense, and the writer and director's creativity is restricted as a result.