Will Java 3D replace VRML?
Java 3D provides a runtime 3D API, first and foremost. You can do more programmatically with Java 3D, but you probably don't want to build all your content (3D models) by assembling nodes in your Java 3D code. For a realistic and complicated world, you probably want to build your models (or have someone else build them) using modeling programs.
VRML certainly isn't the only file format choice for 3D content, but it is a good one: It is an ISO standard, and it was designed for the Web from the beginning, so it's fairly compact and browser-friendly. If you create models in VRML, or in the follow-on XML-based Extensible 3D (X3D) graphics markup, you will be able to load your content in your Java 3D applications and simultaneously repurpose it for Web sites and other uses.