The standard for MST's seems to be to put one or two lines of agent/character dialogue in between every line of fanfic dialogue.

I think that this is a mistake - it only serves to make reading the thing too disjointed. With video commentary you are given two types of input: audio and visual. This allows you to get a gist of how the story goes while you hear the snarky commentary. In a completely written work you don't have this.

I'd say it's better if you lump commentary/story into larger sections each. Say, a paragraph of narration or a large chunk of a conversation, then then a small exchange of character dialogue. This also is an exercise in elegance - jokes become rarer, and you are forced to go with quality over quantity.

To go along with the current discussions going on in the PPC forum, this might also reduce the instances of characters commenting on potentially hurtful statements directly to the author.