Graduate school is a big struggle for many people (I struggled!).
Why is that?
I think that the fundamental challenge that graduate school presents is this: it mandates a shift from being “reactive” to being at least somewhat “proactive.”
In undergraduate work, there are some choices available to students (such as which classes to take and when to take them), but once in a class, the range of choices are narrow.
Take for example an undergraduate genetics class. It will present a series of “facts” to the students and then present them with a series of “assignments” to complete. Students are mostly controlled by the circumstance of that class. There is little choice offered in most classes about what to learn or when to learn it. There is usually very little discussion of open problems in the field. By conveying knowledge as a series of facts, students are expected to be passive consumers and regurgitators of knowledge. (I realize that there are exceptions to this generalization, but this does reflect the experience that I had in at least 90% of my undergraduate classes, and I suspect that I’m not just part of some statistical fluke).
Therefore, students gaining their undergrad degrees – unless they’ve had other independent experience – have no training in how to be “proactive”.
And the single most important thing that you must do to get a PhD is learn to be proactive about you science. You must be motivated to become an expert on your topic. You must be motivated to get papers out on your topic. You must gain the confidence in yourself that you can stand up in front of a (potentially critical) audience and discuss your knowledge and your science. You must believe that you can defend your point of view.
I think the fundamental reason that this transition is so difficult for many people is that we have no prior experience in the “proactive” mindset. We don’t get it from school. We don’t get it from college. We don’t get it from television. We don’t get it from movies. The only source for this would be if we got really lucky and had exceptionally insightful parents (or unusual circumstances).
This may be why people who go out in “the real world” after they graduate from college, then come back to graduate school later, are often quicker to adapt to graduate school life, and not struggle at it so much. The “real world” requires at least some proactivity to survive (though one can get by with surprisingly little). And going back to graduate school also requires proactivity – the willingness to sacrifice a job for five or six years of working on an education at only a bit more than minimum wage.