Sorry if I'm missing an obvious answer somewhere, but what's the difference between the Legacy version and the regular version?
Viewing post in Jimmy and the Pulsating Mass comments
That's an old naming scheme that I should adjust, actually. But, the "regular version" is just the game run through an interpreter called "mkxp." Mainly, it will just allow you to adjust the screen size as if it were a window. The "Legacy version" will let you switch between a few set screen sizes.
Edit: I changed the display names to make this a bit clearer. Really, either version should work just fine.