There is a controversy when it comes to visual effects in the film industry. The common belief is that filmmakers rely too much on visual effects in order to entertain and audience. On the same token, visual effects is often exclusively associated with CGI. Wikipedia writes that there is more to visual effects than CGI. That said, the question is about prioritizing visual effects and figuring out where it should fall when it comes to filmmaking.
The answer to this question is that it depends on the type of movie that the filmmaker wants to create for the audience. In certain genres, visual effects should naturally be higher in the list of priorities. For instance, it is more forgivable for an action movie to rely on visual effects than a drama. Science Fiction is where visual effects belongs the most. With Sci-Fi, visual effects is needed to tell the story.
Visual effects artists like John Textor have worked on plenty of Sci-Fi films such as Transformers and Tron Legacy. They take the time to bring out the best effects for the films that are produced.
When it comes to the priority of visual effects, there is no perfect answer. It is better for each filmmaker to determine the place of visual effects in his film.