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Just found out, Java 3D gives you the option to use the scene graph but also has an immediate mode which bypasses it.[/quote:138aa2cc50]

Not sure if this is 100% true from what they say in the docs?

This scene graph can be minimal and not noticeable from an application’s perspective when using immediate-mode rendering, but it must exist. http://java.sun.com/products/java-media/3D/forDevelopers/J3D_1_3_API/j3dguide/Rendering.html#47302%5B/quote:138aa2cc50%5D

Anyway, if you decide to use immediate mode, then are you really using Java3D..?

JAVA 3D is fundamentally a scene graph-based API. Most of the constructs in the API are biased toward retained mode and compiled-retained mode rendering. http://java.sun.com/products/java-media/3D/forDevelopers/J3D_1_3_API/j3dguide/Immediatea.html#47576%5B/quote:138aa2cc50%5D

I would say that if you find yourself using the immediate mode, you have probably answered your original question:

For my main research paper I’ve decided to explore the reasons why Java 3D is shunned when it comes to games programming.[/quote:138aa2cc50]

If you are going to go down that route, of dropping most of java3ds features, why not just use OpenGL bindings for java or similar?
Eg: https://jogl.dev.java.net/
That’s probably going to be faster, less overhead… and probably be easier to port to a faster language later as well.
Again, haven’t really used java3d myself, and I’m no expert in this area, so would be curious to see what you end up doing.