I don't mess with 3D, so my experience probably won't help you.
The tools I use for working with blu ray are:
AnyDVD HD for decryption/ripping the entire movie to the hard drive (includes menu structure in either files or in the ISO output)
VirtualClone Drive for mounting ISO files
BD Rebuilder for compressing to fit 25gb output (and occasionally an mkv or dvd-video of the main movie only)
ClownBD for selecting sections I want to keep, or combining split m2ts files for the main movie (ClownBD is a gui for tsMuxeR and eac3to)
BDInfo, mostly to identify the playlist file that contains the main movie
And there are many other tools that I have tried on occasion, but I work with main movie backups. I'm quite happy to get rid of the blasted menus.
If you are looking for an alternative to BD Rebuilder, I don't know of another program that will compress blu ray and retain the original menus, other than DVDFab. Slysoft has been working on a program like this, called CloneBD, but I haven't seen any postings with a predicted release date.