I've used both products. They each have nice features. I like the interface and transcoding quality in CloneDVD2, but it started making coasters on me, so I stopped burning with it entirely. I burn with Roxio's "Disc Copier" inside EMC7 and it works great.
A feature I really like in DVDShrink is the ability to select compression levels for individual titles. I care about the quality of the movie itself much more than the "extras". In DVDShrink I can frequently pick "no compression" for the movie itself, and then select a few extras I might want to keep and let those be compressed.
DVDShrink then produces a dvd that plays all the items in sequence (extras after the main title), without running to the player menu to pick a different "title" to play. I think I read that CloneDVD2 recently emulated that capabilitiy in their latest release.
And lastly - about this new supposed "copy protection". Are we sure this isn't just poor implementation of internal "branching" techniques in dvd's where someone wants to let you select the theatrical release vs. extended/alternate scene versions? Aren't the problems occurring only in those titles attempting to employ dynamic branching inside the feature? Like "The Forgotten" and "Ray" and "The Grudge"? My original of "The Forgotten" plays terribly - loaded with pauses, etc. if you choose the "extended/alternate scenes" version. I'm suspecting this is a quality issue with Sony/Columbia/Tristar dvd's. It certainly isn't effective "copy protection" unless they don't care if it even plays properly either.