The Mega Man series is a pivotal series, one that definintely helped Nintendo solidify their lead against the more powerful Sega Genesis and NEC Turbo Grafx-16 back in the day. Capcom knew what they had on their hands, and many would say they milked the hell out of it. While this is not an official game, this is a ROM hack, a game that is made using another game as the base and replacing something from the original to make a unique experience. Many ROM hacks are simply a swap of colors, maybe some level editing or in the case of My Little Pony, complete overhauls.
My Little Pony: Dr. Discord’s Conquest is a complete graphical overhaul of the Mega Man 3 game. Sprites have been changed, levels reworked and bosses are, of course, different. This is a labor of love, just look at the video for proof of that- this is not a rush job.
Since Capcom has not released Mega Man III as freeware, we can only link to the My Little Pony: Dr. Discord’s Conquest patch file over at Romhacking.net