I have recently been testing the shout clear skies and I found out that the first word has the knock down force of FUS RO if aimed at an enemy. Also it only takes 3 seconds to recharge, was it meant to do that? I think it sound like Alduins Meteor word shout.

I'd say it's intentional. You're using the thu'um - a burst of pure energy, like a very powerful spell. One would assume that that raw energy would have some sort of effect on others, even if only minimal.

I've wondered about this as when I'm on the way up to see Paarth it's not uncommon for an unnoticed mountain goat get into the path of the Clear Skies shout. When this happens the goat doesn't get hostile as though I've attacked it (I presume they would do so if provoked) however I do get a health bar for it that shows diminished health for a time. I once felt so bad about it that I chased the little guy around for several minutes trying to cast Healing Hands on him.

Up til that happened the first time it never occurred to me that a "non combat" shout like Clear Skies would do anything to the health of someone who got in the way of it, but apparently it does.