[dnanian]

The new Apple Transfer Assistant works very well for most people. But it doesn't transfer all applications properly, nor does it handle every kernel extension and the like.

If you want to take the purchase of a new machine as a way to 'clean up' your system, it's great. But if you want everything to just "come over" as quickly as possible, the clone works better. (Of course, if it's something like the Mac mini that ships with a build of the OS that's not available elsewhere, you don't have a choice -- you have to use the assistant.)

When you boot from a clone, applications that store aliases have the volume name in the alias along with the folder 'path'. So, when they resolve the alias, you want them to resolve to the clone -- or the new drive -- rather than to something less convenient. As such, it's best to name the clone the same as the drive it was copied from -- that way the aliases resolve to the new boot drive preferentially.

Hope that helps.