I always hate commenting on these remake vs original threads ... I find the remakes to be outstanding and don't want to seem like I'm nitpicking.
I did find the flippers to feel a bit different. Does AFMr use the Williams optical flipper boards or does it use leaf switches? If they're using leaf switches, that's more than likely the difference. The optical flipper switches seem to have a bit more mechanical resistance. You could probably get the exact same effect using slightly stronger springs with the flipper buttons.
Also, someone mentioned dialing the flipper power back ... I agree 100%. AFMr is a lot easier with flippers set to full power. Is there a tournament setting for the flippers on AFMr?
Outside of that difference, the games are identical. The people that bitch about the remake probably got pissed that their original came down in price and are taking it out on AFMr fans.