You could always download the question bank and compare it
I still use my version 3.4 for creating quizzes for my students.
I think (very loose opinion) that historically the changes tend fall into three categories:
Major Revision. Like when Part 61 was rewritten in 1997 or airspace change to the ICAO alphabet or METAR and TAF started being used. Everything you used to know is wrong and the software in these areas becomes virtually worthless.
SSDD. Newer, better (sometimes worse) questions get written but the basic information is the same. Unless you're trying to memorize, the old questions are fine.
Spot Changes. Sort of like the PTS changes this past summer. There are probably questions now on steep spirals, the new definition of slow flight, and more questions on runway incursions and TFRs than there used to be. But since you're working on your CFI, you probably tend to keep up with them anyway.
I suspect that most of the changes that are in 4.0 fall into the SSDD and Spot Change category. You know that since 2000 there have been changes. Airport security, runway incursion emphasis, PTS maneuver additions, deletions, etc, more reliance on GPS and understanding it. All of these are probably reflected in the question bank.
In addition, although some of us tend to discount the value of the knowledge test (I'm one), changes in the test tend to reflect changes in FAA emphasis, which is also reflected in the areas that the FAA wants inspectors and DEs to focus on in the Practical.
Question is, how comfortable do you feel with the older version? If I were studying for the CFI, and using the software as my primary study tool, I'd probably go with the latest.
