I think the use of VCLs in the future with Siteworks will help address this issue because I believe by default it exports the 3D data that composes the surface. Similar to a LandXML but smarter.
I agree the 3D lines are useful but it is always hard determining what is valuable and what isn't. The lay sorting in SCS900 also was not sorting alpha-numeric and made it hard to turn of specific layers. This has since been addressed in Siteworks and is a lot easier to turn on and off unnecessary linework.
I have found it is easier to export the 2D linework and drape it over the surface. We are still learning but at the moment this seems to work well and we don't get too many issue with user missing data.
I may pick your brain on some modeling ideas at another time.