JakeSoft:
I once thought as you do. In fact there is an ADXL335 motion manager included in USaber as well. I used one for my Mk. III and Mk. IV systems. Once I understood the register map, these issues you mention were quite easy to overcome. The beauty of DIY is you can use whatever you are comfortable with. I actually have an ADXL345 in my parts stash that I'll probably add support for at some point too. I like options.
Your LightsaberOS is indeed a great project, packed with options. I didn't use the ADXL345, because of the I2C protocol, which brings me to the same issues as the MBU6050.
Sorry if that has already been explained before, but why exactly did you remove the power saving mode? Was it the I2C, or something else.
BTW, I am studying a few papers on Li-Ion battery state-of-charge estimate, in order to build a proper power management. I'll share the results with you once I have something to share.