I found LunarIPS patches roms the best. Use Megaman v1.0 (U) version with headers for labeled IPS/BPS patches and Rockman X for Japanese version of the game. The edit I made was adding the leg capsules to the introduction stage in Megaman X/Rockman X. 

Updates:
In version 1.0 of the patch I was not able to get the leg capsules to show up how I wanted when starting the game using a password. In 1.1 I was able to finally fix this issue so they show up in either scenario.

I'm not sure why the MMX-Generation patch had trouble displaying the dash animation. It looks like Sophia edited some of the ASM/hex. I didn't check the palettes to see if maybe she tried to have MM dash without the leg capsules (just blue legs). I thought it was very annoying though and would prefer to play the game with proper sprite animation.

Known issues:
This patch doesn't seem to like Zsnes very much. It will crash during the introduction stage. Either use another emulator like Bsnes or Snes9x where this issue doesn't occur, or use passwords to skip the introduction stage. Other bugs written by Sophia are still unfixed. This only addresses the missing leg capsule sprite animation.