My $.02 . . .
While it is true that DVDShrink cannot deal with the unreadable sectors being shoved onto commercially pressed dvd's as a way to attempt to thwart ripping programs, CloneDVD2 has no abilities whatsoever to rip commercially pressed dvd's at all, so that is a bit of a moot point. I have never attempted to rip a title in DVDShrink with AnyDVD running in the background, so I cannot comment on whether that works or not. You can use DVDDeCryptor with AnyDVD in the background, as long as you set up DVDDeCryptor correctly.
DVDShrink generally requires a fully compliant dvd structure to work with the title, while CloneDVD2 is able to deal with the occasional problematic issues left behind when AnyDVD is used to handle the unreadable sectors. Slysoft has been pretty good about addressing those issues when they are identified and they have the time/resources. It seems to me that FixVTS is the solution to most of this nonsense garbage left behind by unreadable sectors.
Addressing the original question - I believe DVDShrink's transcoding engine, when using "deep analysis", results in superior video quality when compared to CloneDVD2. It becomes more evident as the compression level increases. If you are working with a title that needs only a small degree of transcoding (say 90% of the source files sizes?) I doubt that anyone would see a difference in the output of the 2 programs. DVDShrink has many reauthoring capabilities not available in CloneDVD2. The one feature that CloneDVD2 offers that DVDShrink cannot match is the ability to reauthor a title and retain menus. DVDShrink's "deep analysis" is surely much slower than CloneDVD2's transcoding engine. However, it runs pretty quickly on today's dual-core processor based computers, since it is able to take advantage of the power of dual core cpu's.
So - pick your re-authoring/transcoding tool according to your needs and priorities . . .