Hi, I just found out how to make it work with Project M 3.5!!!
1- Download PM 3.5 Iso builder : mediafire .com/download/7p1q0s479pube8e/Project+M+3.5+Netplay+Build.zip
2- Extract it and place Brawl iso inside it
3- Copy the folder projectm from the Smash 3 package and replace the projectm folder from the ISO builder folder.
4- Run Build_ISO v3.5.bat as an administrator
5- Play the new file Project M Community.iso and voila
Notes: I'm using Dolphin emulator and only tried copying the characters from the fighter folder when it worked.
PM Netplay ISO Builder Guide: smashladder .com/help/windows