Opps my bad, the motherboard fuse is between the power supply and the 220uF power delivery capacitor so the motherboard current protection can not trip. Still that is a lot of 10uF caps that will have to be pulled up during hot-plug. This Intel design guide shows a 220uF Capacitor (with ESR warning) used for USB power delivery:
http://www.usb.org/developers/docs/whitepapers/power_delivery_motherboards.pdf
When the hot plug happens the ESR will drop the voltage which is fine as long as the power recovers without oscillations, so I think the 3V3OUT bypass and the ferrite bead will help. But you may consider using the PWREN pin and a P-ch MOSFET to prevent powering everything until after USB initialization (that is what I am doing).
One other thought is the DTR reset interface, after looking at it some time back... well it needs a diode shunt to be safe (page 5):
I can't find the forum thread now, but it was a good read, the concern is that if the RESET pin is taken to 12V it is guaranteed to be in parallel programming mode, but no one really knows if the 10V that the DTR capacitor will put on it is enough to trigger that mode (and a lockup).
EDIT: this may have been what I was looking at...
http://forum.arduino.cc/index.php?topic=64256.105