I actually enjoyed the latter a whole lot more, because they seem to have decided about fifteen minutes in to simply have fun with the idea. The Meatrix, on the other hand, makes Triumph of the Will look subtle by comparison. Plus it just wasn't funny, though it was very nearly saved by the presence of a chicken in sunglasses.
You're right that the Meatrix isn't very subtle. It is, however, fairly accurate. Had they decided to just slap up a Web page talking about factory farms, antibiotics, inhumane conditions, etc., I doubt that many would have bothered. At least in its current incarnation, I know that it has been spread around quite a bit and many more people are aware of those underlying issues.