What version of flash do you intend to use? What is your target audience (broadband, dialup, yarn)?
I’m working on a similar problem. I’m about 99% sure that I’m just going to use MX2004Pro to convert me .mov into and .flv and stream it through me swf. I may be sacrificing dialup users though. I hate them, but I have to recognize that, like the Amish, they still exist (I don’t hate the Amish though).
For my animation (I posted it here a couple weeks ago) I use the toon render. I love using the toon render and with flash as my intended conveyance, toons have the benefit of using far fewer colors. So the initial filesize, even using the animation compressor in quicktime is relatively small. I was advised to check into the plugin you mentioned, so I contacted Marcel, the author about a specific question I had concerning toon renders and toon outlines. Since I wanted to keep the outlines, he suggested that I use something other than his plugin, because if I was already attached to the way it looked, then usig his plugin would change it (and not really do the outlines I wanted).
So if I had anything useful to say in short, it would be to use MX2004Pro and compress normal old AM .mov output to a flv and stream that.