Perhaps the most straightforward and effective way of enhancing and individualising a 3D integrated mesh is to drape a 2D polygon layer over it.
This is achieved by simply dragging an appropriate polygon layer into the ‘2D Layers’ section of a project that already contains a 3D mesh object. ArcGIS Pro will automatically handle the draping and will also enable its interactivity, upon clicking individual features, by default. You can still style the draped polygons using the standard Symbology interface. When combining polygon layers with an integrated mesh, you’ll likely also want to adjust the layer transparency, so that both sources remain sufficiently visible.
A thinly populated (or heavily filtered) polygon layer can be used to achieve an effect that’s analogous to drawing on the mesh with a highlighter pen. This just requires an adjustment to the polygon layer’s symbology (maybe choose a neon-type colour…), along with a suitable layer transparency (try 50%). An example of this is shown below:
Rather than highlighting only selected areas of the mesh, another approach is to highlight individual feature classifications using colour/style variations. In the example below, 2D polygons from the OS NGD Land Use Theme have been added to the scene. Using the Symbology tools, these polygons have been styled according to the unique values found with the ‘oslandusetiera’ attribute. A transparency of 50% has also been applied to the entire layer.
Even though draped, these features can still be clicked upon, allowing their individual attributes to be interrogated via a pop-up window.