Since upgraded version (Mega Man X) exsists, it'ss not necessarily practical moneywise to fix the old crap. 
Except X is locked away into a capsule, and judging from Dr. Light's health in the Maverick Hunter X/Day of Sigma stuff, isn't close to being complete yet, since Dr. Light seems a fair bit healthier than he does then.
But honestly, it annoys the ever-living hell out of me, not because they took them away, but did so without giving a reason. A line of two of text somewhere in the intro, in a cutscene, stating that the modules were being upgraded, or even that they had broken, or something. Otherwise, to me, it gives the feeling that Mega Man is basically becoming a jerk, i.e. "I don't even need to use this stuff to beat Wily." I get that they were trying to emulate MM2, but seriously, let the past stuff die now, please? I don't want another 8-bit Mega Man or 16-bit Mega Man X, I want a 2D Mega Man game with some nice high resolution sprites, like we've actually made some bloody progress in the last twenty years... I get that it is nostalgic, but really, in my opinion, it cheapens the brand.