First I must admit, that I believe Shrink is a wonderful program (shh, I hope my boss isn' reading this).
CloneDVD can do a lot of things Shrink can't and vice versa. Most of the time I use CloneDVD, and on some occasions Shrink. They complement each other nicely.
For example: Removing material while keeping menus sucks with Shrink. CloneDVD2 is clearly the winner - it lets you keep menus, but remove every title you don't want completely, reducing compression of the parts you DO want.
It can split to two discs the way you like it - movie on one, extras on another while keeping the menus working. Or split the movie in the middle keeping the menus.
Shrink accepts the files made by CloneDVD, so you can pre-process the disc with Clone and compress with Shrink (if you prefer Shrink's compressor).