This is a project that me and several others have been working on for the last several years in between things. The premise is that the twenty canon Primarchs and Legions are replaced by fan-made creations, who proceed to decide the fate of the galaxy in their own ways.
There are several other differences from the canon universe as well. The Great Crusade here takes considerably longer - close to 500 years instead of 200. As a result, the Primarchs take larger roles in governing the Imperium, and many end up accumulating vast personal holdings, domains, or mini-empires within the larger Imperium. In addition, all twenty Legions remain in existence throughout the entirety of the Great Crusade and beyond; while some of the Legions and Primarchs are indeed deconstruction of the canon Warhammer characters, others take completely different routes.
For those of you who read "Reaper's War" (posted here), you may have an inkling of what to expect (and there are two other novel-length works set in the same universe, which I may post at some point if there is interest); for others, check it out, and let me know what you think!
http://twisthammer.blogspot.com