I am in the middle of playing Mother 3 using Mednafen. I have noticed that is it rather hard to get the rhythm combo on the emulator. After looking into the issue, I found that it could be helped if the frame skip is changed to 0. 
I tired looking for another thread, and the one that was available said something about using the space bar for GBA emulators. Is that only valid for the VBA? I would much rather not have to start over using VBA. 
If anyone has any information about this, don't hesitate to let me know!
Thank you~

The space bar will put the emulator in fast forward, so I'm not sure if that would help with the rhythm combos. But that is available with Mednafen if you have RGR Plugin 2.10 or above installed (I'm assuming you still have version 2.0 installed).

Also, it's possible to transfer your save file from Mednafen to VBA, if maybe the emulation is better with VBA. You'll need to rename your save file located in your RGR Plugin Data folder, and then move it from the Mednafen directory to the VBA directory.

Open a run prompt with Windows key ( ) and R key and copy paste the file path below.

Windows 8, 7, Vista
C:ProgramDataVizzedVizzedRgrPluginUser-510498Mednafen_newsav

Windows XP
C:Documents and SettingsAll UsersApplication DataVizzedVizzedRgrPluginUser-510498Mednafen_newsav

In that folder find the file Mother 3 (japanese to english translation).ce5c7ba6fbe648e6d65d77030151d6f5.sav and rename it to Mother 3 (japanese to english translation).sav then cut the file and paste it into this directory:

Windows 8, 7, Vista
C:ProgramDataVizzedVizzedRgrPluginUser-510498VBASaves

Windows XP
C:Documents and SettingsAll UsersApplication DataVizzedVizzedRgrPluginUser-510498VBASaves

If you want to transfer the file back to Mednafen, rename it to the original name with the hash numbers at the end and move it back to the Mednafen directory.