Timecop's port of Multiwii to STM32 should work on the PX4 with some changes to put the mpu6000 in to I2c mode and use it as a Mpu6050 ,or a new Multiwii driver for Mpu6000.
The latest version of his Naze32 is using the Mpu6050, HMC5883 and MS5611 sensors running the ported Multiwii.
To start I have experimented with many of the available boards over the last few years from the KK to the APM2. including allinones with Multiwii , Freeflight/Naze32 with FF2 and multiwii( baseflight).
I have a APM2 setup and a MegaPirate on 2.8 with a 2560 board and Mpu6050,HMC5833,MS5611 using the Gy86 IMU.
The MegapirateNg flys very well and I would say as good as the Apm2. I built my own Data Flash board and added it to MegaPirateNg
I have also used Multiwii on the same setup with less impressive results.
The Multipilot/Vrbrain and the Arducopter32 port as best I can tell only runs on the oilpan and analog sensors ! I can not find the page right now but did see a sugestion that arducopter32 would run on the PX4 which may be possible with an oilpan! This same google page for the Px4 also called for a architecture discussion for development going forward.
A STM32 MPNG using MPU6050/6000, HMC5833,MS5611 would be a very good addition to the available options and allow the Px4 to fly while development progresses on the new code under rtos.
I will be playing with a STM development board and GY86 IMU and maybe a PX4 and would welcome any input.
I had not looked at Areoquad for a while and I see Areoquad32 software has these sensors confiureable and MPU6000 interface selectable as I2c or Spi , wouldn't that be great on arducopter !
So it looks like the next project will be Areoquad with a Maple board and the Gy86.