The National Geospatial Intelligence Agency has released the following advisory about the use of Web Mercator map projection: http://earth-info.nima.mil/GandG/wgs84/web_mercator/
While Web Mercator is quite useful for web map services by dividing the earth into perfectly square tiles regardless of map scale, it was not intended for navigation or high-accuracy mapping. Even before this NGA advisory was released, I had been concerned about relying on tools like Mission Planner that use web map services such as Google & Bing. I do flight plan edits in commercial GIS software because there's more control over reference systems & the ability to use higher quality datasets.
I'm curious to know if anyone else is using alternative methods for flight planning. Or am I simply mistaken in assuming that Mission Planner does not reproject into the WGS 84 based reference system?