After some looking I decided that svg writing would be the way to go. There is an svg exporter on the file exchange but I think it is poorly organized and doesn't create files that are amenable to editing in Illustrator.
I had started to create my own implementation of a svg writer which would work to organize things a bit more but I've since moved on to trying to graduate.
That being said, supposedly Waterloo graphics has put some effort into this problem. I haven't tried it yet. Here's an article that mentions it and specifically working on figures in Illustrator.