So what is the main difference between what Honda ran on there private bikes, compared to what all have to run in 2016
this is the best description i can find https://motomatters.com/analysis/2015/09/08/everything_you_wanted_to_know_about_moto.html
That article covers it pretty well. To sum it up quickly the major difference was the old software was written by by some of the best chassis dynamics engineers in the world specifically for their bike. The new software was written as highschool science fair project that makes everyone happy, or not.