What I'm showing here is when you move, the collision box and the player aren't 'sync' together. There seems to be a slight delay of the sort.
doing some testing, I was kind of able to fix this. However after doing so, when you move forward, either the player or the screen kind of moves a bit shaky. This was an issue from before thought to be 'fixed' now, so I don't know what else to do. ![Sad :(](http://forum.rockmanpm.com/Smileys/default/sad.gif)
I don't think it's really a problem. In MMR the collision boxes and sprites themselves have this problem, although the player can't see it, and no one has complained about it after a month of the game being available for download.
If you really want the problem alleviated, did you try using a fastloop to set the position of the player sprite? What I did was set the player sprite's position to the collision box instead and had all the movement attached to the collision box and I scroll the screen based on the collision box rather than the player sprite.
Do you mind if I add you on MSN Messenger? I can perhaps help you out with things a little since I use MMF2 as well.
Also, as for the Wily sprite, I think the NES did it that way because of the sprite palette limit on the NES as others mentioned. Although, you aren't working with NES limits.
![Wink ;)](http://forum.rockmanpm.com/Smileys/default/wink.gif)
The sprites in the sheet however wouldn't be possible on the NES, unless you used an additional palette for them, because sprites on the NES can only have 3 colors per palette plus an additional transparency color.