Version Differences

Weapon Get Cut Scenes 
 The most obvious difference between the US and Japanese release of the game are the cutscenes after clearing one of the 8 robot stages. On the US cart, you only ever see Dr. Light talk to Mega Man. On the J cart, you can see any of Dr. Light, Roll, or Auto. 
 Dr. Light is always the fastest conversation. Auto is usually the longest. The notable exception is "Burst Roll". 
 Timing Differences 
 Data courtesy PJ. Better Formatting in progress  
 Bass dialogue 
 
 
 
 Segment 
 NA (time) 
 JP (diff) 
 JP (Light) 
 JP (Auto) 
 JP (Roll) 
 JP (Average) 
 JP (Best) 
 JP (Worst) 
 
 
 Intro 
 123.278 
 -6.922 
   
   
   
 -6.922 
 -6.922 
 -6.922 
 
 
 Bass Dialogue 
 12.995 
 -0.216 
   
   
   
 -0.216 
 -0.216 
 -0.216 
 
 
 Cloud proto 
 14.459 
 -0.765 
   
   
   
 -0.765 
 -0.765 
 -0.765 
 
 
 Cloud weapon get 
 27.521 
   
 -3.611 
 0.799 
 0.666 
 -0.715 
 -3.611 
 0.799 
 
 
 Junk end load 
 2.446 
 -0.017 
   
   
   
 -0.017 
 -0.017 
 -0.017 
 
 
 Junk weapon get 
 28.686 
   
 -3.943 
 1.032 
 -0.566 
 -1.159 
 -3.943 
 1.032 
 
 
 Freeze weapon get 
 26.306 
   
 -1.048 
 5.075 
 3.278 
 2.435 
 -1.048 
 5.075 
 
 
 Burst weapon get 
 27.754 
   
 -4.210 
 2.363 
 6.872 
 1.675 
 -4.210 
 6.872 
 
 
 Pre-museum lab 
 49.900 
 -11.913 
   
   
   
 -11.913 
 -11.913 
 -11.913 
 
 
 Post-museum lab scene 
 7.338 
 -0.383 
   
   
   
 -0.383 
 -0.383 
 -0.383 
 
 
 Turbo proto 
 14.093 
 -0.599 
   
   
   
 -0.599 
 -0.599 
 -0.599 
 
 
 Turbo weapon get 
 25.973 
   
 -1.414 
 2.047 
 3.311 
 1.314 
 -1.414 
 3.311 
 
 
 Shade load 
 19.651 
 -0.050 
   
   
   
 -0.050 
 -0.050 
 -0.050 
 
 
 Shade proto 1 
 18.486 
 -3.611 
   
   
   
 -3.611 
 -3.611 
 -3.611 
 
 
 Shade proto 2 
 36.106 
 -2.313 
   
   
   
 -2.313 
 -2.313 
 -2.313 
 
 
 Shade weapon get 
 28.486 
   
 0.150 
 5.724 
 2.529 
 2.801 
 0.150 
 5.724 
 
 
 Slash weapon get 
 23.910 
   
 0.083 
 4.509 
 6.123 
 3.572 
 0.083 
 6.123 
 
 
 Spring weapon get 
 27.920 
   
 -3.877 
 1.464 
 -0.266 
 -0.893 
 -3.877 
 1.464 
 
 
 Lab cutscene 
 76.456 
 -6.805 
   
   
   
 -6.805 
 -6.805 
 -6.805 
 
 
 Bass 1 intro 
 10.532 
 1.980 
   
   
   
 1.980 
 1.980 
 1.980 
 
 
 Bass 1 end 
 7.754 
 -1.864 
   
   
   
 -1.864 
 -1.864 
 -1.864 
 
 
 Bass 2 intro 
 18.885 
 1.697 
   
   
   
 1.697 
 1.697 
 1.697 
 
 
 Bass 2 end 
 8.719 
 2.629 
   
   
   
 2.629 
 2.629 
 2.629