Sure.
http://gbatemp.net/threads/ssbb-mod-iso-builder.351177/
Follow the instructions in this thread, but make sure to download the file from Reply #1 first and then replace the .bat file with the one from Reply #18 for ProjectM 2.6b
Addenum:
1.) You need the Riivolution.zip of ProjectM
2.) Open the .bat and change the GCT size for ProjectM to 9100
3.) Until the .bat is updated for ProjectM 3.0 this won't work for ProjectM 3.0
EDIT: Ignore error messages during the merging process, those showed up for me, too but nothing actually happened