The new PX4 Pixhawk module is an evolvement of the existing FMU and IO modules and completely compatible. The main difference is the target audience: While the FMU and IO stack is super small (the size of an average 8 ch RC receiver) but in some ways almost too densely packed, Pixhawk has more space, more serial ports and more PWM outputs.
As the above picture shows, there are two groups of servo connectors, one main group of 8 outputs which are wired through the backup processor, and an auxiliary group of 6 outputs directly wired to the main processor. The port labeled "RC" can take normal PPM sum or Futaba S.Bus inputs, the port labeled "SB" can read RSSI our output S.Bus to servos. A Spektrum satellite compatible port is on top (labeled SPKT/DSM).
The basic operation is the same, and the software is shared. Inside Pixhawk a FMUv2 and an IOv2 do their duties on a single board (and developers will find that the software will refer to FMUv2 and IOv2)
The main differences between old and new are:
Both generations offer the same backup / override processor that allows failover to manual if the autopilot fails in fixed wing setups. For software developers the differences are nicely abstracted in the PX4 middleware, and can be sensed / configured at runtime.
Pixhawk is available for pre-order here.