After releasing the mkxp version, some new glitches came to my attention--mainly the black box covering the player's sprite for some players and battle bgm not looping accurately. So, I've switched the legacy mode back to the main branch.
If you want to use the mkxp version, you can still do so. This is set up like a beta now, so just right click on the game in your library, choose properties, select the betas tab, and pick "mkxp" from the dropdown menu. The mkxp version will smooth out framerate issues and the large sprite fix crash, so, if you're running into those issues, you still might want to use the mkxp version.
Sorry for the inconvenience, and thanks for your patience.