The significant difference is that it can map -100% / +250% fuel, where the PCIIIUSB can only do -100%/+100%. This satisfies most fuel needs for most folks most of the time. They are saying we will have a piggyback controller for the secondaries soon, but we have not seen it yet.
As stated, it can map per gear, per cylinder - so you could create 24 separate maps.
Also - all the features of the old Multi Function Hub are built into the unit, so you do not need a Hub to add a map switch or LCD or the Auto Tune, etc...
The Auto Tune also allows you to build a map on the fly when starting with a base map - very nice feature.