Migration Tool VS CCC
Indeed, there are some differences between cloning the disk and Migration Assistant.
As you mentioned, MA will not migrate all the files, which can be both good and bad…


Corrupt system files won't be copied if you use MA since you are installing a completely new OS, then copying certain files over.

However, be warned that since they won't be copied over, any modifications that you've made will be lost. This can be mitigated by manually copying over any system files that you've modified1.
Incorrect preference files will still be carried over, but only if they're specific to your account.

Most system-wide preference files will be reset, which can be useful if you have system-wide problems, but may cause some extra effort if you have specific changes that you've made.

This can be mostly mitigated if you know which global preference files you have modified, since these can be copied over1.
Because CCC doesn't reinstall OS X, the Recovery HD will not be changed.

This means that it won't reset it if you have problems with your Recovery HD or for any other reason, although you can manually copy your Recovery HD using CCC which can be useful if you've made changes to your Recovery HD that you wish to keep.
MA should not copy any system-specific preferences, which can be useful if you are migrating to a different computer, but since you are migrating the same computer, this should not be a reason to decide one over the other.
CCC will leave you a fully-bootable OS, which is much quicker than re-installing OS X then using MA separately.
If an app relies on an HD's unique identifier stored in a certain preference, CCC will not correct this.

Since MA will reset almost all system-wide preferences, any such preferences will not be maintained, and will revert any settings to match the current installation.


In conclusion…


If you want the speediest possible Mac, with all your data and almost all your settings, Migration Assistant is the best way to go.
If you want the simplest migration or want to ensure that all your settings are copied over, use CCC or another disk cloning tool.


1 This is where looking through your backups of system files &amp; preferences before you changed them can really help, because you did make backups, right? :)