Nice visuals only partly make up for sub-par jokes
It just wasn't funny. The pacing was all wrong, with too many frequent pauses. I'm not saying you should be like egoraptor, throwing the jokes out every second, but you need to speed it up between transitions of scenes.
Also, the Navi voice actor isn't that great - every line sounded too sarcastic all the time. The animation is not the best, but it's damn good - the anime moments kinda ruin it for me as I don't find anime funny at all.
I was hoping to see an improvement over last time, but the same problems remain. With the overwhelmingly popular response, it's likely this review won't change anything, but I'd suggest finding a professional writer (or someone with a bit more experience) to write the dialogue, and then you could tweak the pacing yourself - the animation is already at a good level.
I'm not going to be blinded by the Zelda name on the front - it was an average flash in terms of story, pacing and laughs. Not bad, but not awesome, either. Better luck next time.