One of the more interesting features of the Integrated GBA is that it can be used on netplay. In this setup, the Host computer controls most of what is going on, including the savefiles for Every GBA. This means if you are doing a Pokemon battle via Pokemon Colosseum or Pokemon XD, all players involved should send their GBA saves to the host, and every player must have each of the GBA games in a path that dolphin can find. The host is also responsible for renaming the savefiles to refer to each port. In order to enable GBA controllers for netplay, the must configure the netplay controllers and checkmark the "GBA" option for each port that is meant to be a GBA.
Ultimately, the Sys folder should be placed at a location similar to:RETROARCH_SYSTEM_FOLDER/dolphin-emu/SysThere is also currently a bug with this core and the GL driver that can be worked around by going to settings > user interface > show advanced settings ON and then going to settings > core > allow cores to change the video driver OFF.
If the issue isn't present in the latest stable version, which is the first broken version? (You can find the first broken version by bisecting. Windows users can use the tool -emu.org/Thread-green-notice-development-thread-unofficial-dolphin-bisection-tool-for-finding-broken-builds and anyone who is building Dolphin on their own can use git bisect.)