I'm in the process of writing a custom combat system for Skyrim and while the new damage algorithms work nicely, I would also like to add some additional challenge and longevity to melee combat by increasing the chance NPC's block the player's attacks - Skyrim's whack-a-ton combat relies on HP buffers to soak up damage, which I got rid of, but that tends to make fights kinda short and brutal without some deft blocking.

Now, I can script a block as in that the NPC takes less or no damage, but what I want is the full deal - animation and all. Is there any way to do that, or alternatively to increase the chance of blocking for NPC's across the board without the need to go over all the combat packages in the CK?

This probably isn't what you're looking for, but there are combatstyles in the miscellaneous tab (I think? Or maybe the character tab. There ARE combatstyles though). And with these you can adjust how often the NPC blocks and shield bashes and power attacks and regular attacks etc etc. Here is the wiki's page on them http://www.creationkit.com/CombatStyle

EDIT: So if you were to change the default combat styles and the more popular ones (or even all of them as it doesn't take too long), then you would essentially be changing the combat AI for all NPCs.

Yep, that's true - what I'm worried about is that I end up making all NPC's turtle up. Skyrim's issue is that combat reactions of NPC's are kinda slow - compare the melee combat with that of, for example, Mount&Blade, and you immediately notice the difference.
The main problem is that Skyrim lacks proper NPC reaction to attacks. I can try to reverse the offense/defense multipliers in relevant combat packages, and see if that works, but as long as I'm scripting a whole new damage system I thought it could be nice to add some NPC reactions to melee attacks, like a quick parry, for example. It would be just a few lines of code, but needs a way to properly execute animations or it would look weird and confusing.