i've owned and beaten each of the X series games before (still got X, and X6). I think command mission was one of 3 megaman RPGs i ever liked much, the others being the legends games.
i think i only managed to do a perfect run on one of the X games was the 1st game on snes, and i only managed that once. no damage (outside the vile fights where you HAVE to take damage to progress), all sub/heart tanks gathered, all bosses beaten, and in under 30 minutes too, never managed to do it a 2nd time though :/ and that was without a emulator of any kind (not easy to do a perfect run through a megaman game)
hardest game for me would probably have to be 8 out of the classic series, that game has some hard final boss stages but then again the classic series was always hard in general which made it fun
