Hi Gregory !
Fisrt, I'm sorry for my long silence, I've had urgent problems to solve and my MPU9250 was not my priority since september !
I yesterday downloaded your last version of avrcopter, and... It doesn' work 
I use an Arduino UNO, just like you.
When using I2C-scanner, I can find a device at I2C adress 0x68.
I do not use the makefile, but the ide compiler... Is that a problem ?
In your code, I've add #define MPU9250 in inv_mpu.h, and #define MPU_DEBUG in all .h
I get this :
MPU init: 3
Free mem: 208
I've searched were the error comes from.
It happens at the very beginning of the program, at the call of ret = mympu_open(200);
I've searched a bit more...
In mpu.cpp, function mympu_open(...), call to mpu_init(NULL) returns -7
Then, I've found that comes from inv_mpu.cpp, function mpu-read_mem, in wich
st->chip_cfg.sensors equal 0
Have you any Idea of the origin of the problem ?
Many thanks !
PS : have you tryed the MPU9250 ? If not, and if you are interested, I'd be happy to send you one on a breakout board ! 