Hey Brian- thanks for your question!
3D Web GIS, the Scene Viewer and the Scene designer experience is an emerging technology, and we're making it easier for users to apply lessons learned from the web map experience to scene authoring. A big example of this was including the search dialog from web maps in the scene designer in the latest release.
In fact, many of the properties you apply to feature layers (Popups, symbology, filters) persist in the scene viewer. This blog is a helpful overview to getting started viewing your authoritative data in 3D.
Delivering your Common Operating Picture with 3D
Essentially, it's the difference between versions of the ArcGIS API for JavaScript (3.x to 4.x), and we have a lot of work going on here to bring some applications to 4.x to fully utilize scene capabilities.
Happy to talk through any specific needs you might have- thanks!
Philip Mielke
3D Web Experience Product Manager