Oh boy, hope this doesn't start a war, but, just about everything required to be a safe pilot is lacking in some way or another with every student I have seen.
Here is my list, mind you only for private pilot, I cannot comment on instrument/commercial.
Basic knowledge is lacking with core basics*, management**, discipline, weather, systems, aerodynamics.
Instructor presentation I believe is a huge problem. One of my pet peeves is the system we use for delivery. It takes people, on average, 55-90 hours, depending on source, to get their license. Yet we turn around and teach a 35 hour syllabi. Furthermore, we give too many tasks at once, instead of a controlled delivery, allowing students the chance to focus on, and master, one idea. Then they can apply that idea to the bigger picture. For instance, is it really that important that they takeoff in lesson 1/2 before they even can properly taxi, when your likely going to be doing most of the work? IMO its dumb and hinders learning.
*Core basics: Things like, do they coordinate rudders and ailerons in every turn? Does the student keep an active visual scan from takeoff until landings? Can they execute all basic maneuvers, from takeoff until landing, without relying on instruments? Do suffer from fixation, probably the number one killer in aviation and rarely ever focused on with private pilots. Most private pilots suffer from one or more of these deficiencies.
**Management: Are they assertive with the decisions they make? Is there noticeable organization? How is their thought process, especially with emergencies? Do they demonstrate good discipline, specifically as it relates to flight preparation? Again, most students lack one or more of these. General management isn't really a focus of any course, which I find appalling considering a PIC is nothing more than a manager.
This is a list I have been building on and revising since I started writing this course many of you have heard me shouting about on here for months. It is still scheduled to go live in January with a little more info in my signature. I have attempted to include, equally, all of these areas that I believe are lacking in the training environment, and many more, not listed, into this work.