Dear Zachary was quite an experience. I think any movie that can involve me that much is worthy of praise, but I do agree with a few things said above.
Yes, the manipulative nature of the direction was blatant, and at times it was too much (repeating and/or pausing scenes and some of the narration really emphasized the agenda) but it's inevitable that it would be a slanted story. It's a first-time filmmaker's journey into hell, essentially. His emotions are apparent, if not by his own words, by the way he tells his story. It may not be a better documentary because he doesn't let the facts speak for themselves, but it's still good (to me) because he is blatantly a character within the story, too, and he never ignores that fact.
It reminds me of a documentary I didn't particularly like from last year: My Kid Could Paint That. There was a short scene where the filmmaker shoots himself rambling about his personal struggle with how to handle the story at hand, and how it could affect the success of his story. It felt hugely out of place and inappropriate, and was the last straw in what I felt was a pretty forgettable flick. Dear Zachary's director is up front all the time about his intentions and wears his heart on his sleeve the entire time, in the editing, his choices in timelines and the over-the-top music.
I guess what I'm trying to say is, as a viewer, that I knew what he was doing gave me a different outlook on the movie as a whole. If I felt the filmmaker was being subtle or dodgy about his intentions, it would have bothered me more, but all signs pointed to: this is the best representation of how I experienced this crazy CINECAST!ing circus in my life.
I do agree entirely that the repeated use of the grandfather calling that woman a bitch was completely unnecessary. I think it had the reverse effect of what was intended.
Forgive my rambling...