A while back ago I had a similar question in regards to Layer Controls in DWF.
Hello
marchourican
I created this video to help him understand how to turn things on and off in the DWF environment. Ultimately I think that the answer for you is going to be DWF based. You can pack all your views (plan and 3D) in a single DWF file and share that with your customers and your consultants.
There are maniplulations that will allow you to hide and show different objects in the 3D model. You don't have to buy software, MEP and 3D AutoCAD objects work with out a glitch. You get more of the intelligence behind the object properties then you do in PDF. Personally I believe it is more robust then PDF and its free!
Check out this video response I created for Jason Quintana out of Roy, UT.
DWF Layers - Hiding objects in 3D DWF fies