Brono's suggestion is good, and I too believe by skipping the user, you did pretty much tell it to skip most everything. This is due to the assistant wanting to migrate what it sees as "personal data" into the users home folder, instead of scattered across the drive.

One thing to keep in mind, migration assistant does run as part of the initial OS setup after a clean install (or after unboxing a new Mac). This saves needing to create a temporary user, assuming you choose to go through the process then.

I'm also not sure how the assistant treats data from a Windows machine. This is a new feature with Lion, and I've never had any hands on experience with it. My guess is it's probably pulling from the most common locations the Apple Geniuses found data when doing PC to Mac migrations in the stores.