The problem it boils down to is ease of communication. When you develop a new synthetic pathway, or you find the newest cancer drug, you want to tell the whole scientific community about it, and the medium for that is scientific articles, published in scientific journals after rigorous peer-review.
Those articles were traditionally printed on dead trees (i.e. paper) and are now mostly just read on-screen in PDF format. With both of these cases, it is not easily feasible to include 3D visualisation more than what is already done in class on a blackboard. Wedges, bold lines and parallel perspective are used all over the world and they mean the same thing. We already have a system that works well enough, why change?
I too sometimes run into the problem that I cannot easily visualize the 3D structure of some molecule. Then I build it from a model by hand, or on the computer. Those few cases where I had to do that simply do not justify the overhead if you want to do this for every molecule.
Surely a better system would teach everything in 3D first to gain a true visual and theoretical understanding of the subject, and ONLY THEN taught in 2D on how to simplify things for proper communication?
You are absolutely free to teach organic chemistry the way you want to. But you will then see, that this generates a bunch of work for the set-up of that system (figuring out which software to use, writing guides for the students to use the software) and basically everyone needs a screen in the lecture hall. A blackboard is readily available, easily erasable and as such the best option.