A flowchart of the GAME and not the STORY works for me.
First I set some general rules (say 2 characters and 5 endings, 40 minutes of play). It is critical to do this BEFORE thinking about your plot/story, because once you start writing, the size of the game can grow exponentially. You must have limits.
Get an idea for what is about to happen and write within that framework, rather than trying to cut-and-paste as new ideas come up.
... what he said ^_^
Depending on the complexity, I usually draw a sketch of the plot branching and then refine and redo it a few times (not too many, though). Once this terrible part is over, I can start thinking what kind of plot would suit that type of game set-up. I know I will have say 5 endings and 20 path possibilities and try to think about the setting (also dependent on the resources) and graphical layout. Once this is more or less established, I can focus on the story.
Personally, I never ever make any character designs before the story. Many writers have character-based stories, where they design a character and let it act and interact in an environment. I have a different approach, as I don't want to present a character, but certain emotions. I decide on an emotion and then think of how I could best present it. In Black Pencil it was loneliness. In River Trap it was the question of loving the person inside. And in Kaori, it was letting go of the past. You can see my characters don't really have any special characteristics such as "outgoing" or similar, because of the story-writing style. The drawback is that the characters have less charisma and the plot often goes in an inevitable direction. (sorry)
So I think you can make it work with any of the suggested systems, just try them all out and see what works for you. And back on topic, when things get too complicated with the script, I use the Outline function in MS Word. It lets you do up to 9 levels of hedings and sub-headings, if you require.