I have found a way to do this with no extra steps in my workflow.
Open Image Capture. Open Image Capture Preferences. Choose "Image Capture" for "When a camera is connected, open: " Close Preferences. Click Options. Check "Delete items from camera after downloading" and "Automatically download all items". Click OK. Choose "Aperture" for "Automatic Task:". You may select any location for "Download To:"
Now your system is setup correctly. To see this in action, close Image Capture and Aperture if they are open. Connect your iPhone and Image Capture will open, it will import your photos, delete them from your iPhone and close. Aperture will open and import your photos to a new Untitled Project. You will have to find this project and manually rename it. I am unsure if Aperture will split the projects correctly, but I'll find out in a few days.
It would be nice to have this as an option in Aperture 3, but this method seems to work well in the mean time. I hope this clears up any confusion.