If you clone as your primary backup method, then you should have two external HDs instead of having one HD that is partitioned.
So if you have a 200GB internal HD that you want to clone. You should get two external 200GB HDs for cloning and not one 400GB HD that is partitioned. By having 2 HDs you increase your redundancy. If you only have 1 HD, and it dies mechanically, both partitions (clones) will be unusable.
Likewise if you decided to have only one external HD to hold your clone, you are now vulnerable during the cloning process. So for example, during your cloning, the external HD fails mechanically. You say to yourself, no worries, I have my internal HD and it's working fine. The next day you go to your local computer shop and purchase a replacement HD and begin the clone process. Unfortunately, your internal HD decides to fail mechanically. Now you have no backup.
BTW, this happened to me.
Data recovery places are expensive. Plus they may not be able to recover all of your data depending on the type of mechanical failure. Ever see a HD that is scratched?
The best way if you are going to cloning as a backup method is to have two separate HDs and then clone alternating between each one on a regular basis such as weekly, or more often.
I've had to restore from Time Machine several times due to flaky OS X updates from Apple. I've also used Migration Assistant from a Time Machine drive with success.
I know that it works for many. But to me, my backup system has to be 100% otherwise why do it.
I've tried it as well, although not to the extent that my friend did, and it failed on me as well.
I do not trust Time Machine. For me cloning is the way to go.
Also, one nice thing about cloning is that you can boot from the external and do drive maintenance on the internal. Much faster and easier than booting from CD.