Even if Software-Systems have a certain complexity, the goal should always be to break it down to simpler processes. So it's good to separate major from minor requirements from the beginning of the project. Lastly you would like to have Software which is extensible and easy to maintain.
Modern Software-Development methods like SCRUM allow us to keep the development processes lean, so you can concentrate on the main parts. Unfortunately you see SCRUM at it's best only in a minority of companies, because their internal processes or the processes of their customers are not fully adaptable to the rules of SCRUM. So it might happen that mixed forms of SCRUM cause more complexity than they help to simplify them. Sometimes there is also no time or courage to do things different than normal.