Hey there!
I tested Metroid Fusion on the emu and on my NDS, it saves without issues. You could have issues with your battery, see the troubleshooting docs (
https://superfw.davidgf.net/docs/usermanual/troubleshooting/#bad-cart-battery). Feel free to suggest any new troubleshooting documentation if you discover any workarounds.
I think that some people have issues with Supercard and SuperFW and they cannot boot almost any games. I would recommend to run the tests (SDRAM, SRAM, etc) to ensure the cart has a working memory device. Even in that case, there's people who have reported issues with their carts and games known to work well. I would suggest you to test some of the most played GBA games (ie. the top 10) and report if those work. If those don't work, it means there's something wrong with the cart or the device, or there's some bug with SuperFW. There's a lot of people happy and a bunch of people who cannot use SuperFW successfully, unfortunately I cannot reproduce any of their issues, therefore I cannot fix them.
As it was already explained, you could chainload the firmware (SCFW has a minimal bootloader for instance) but I recommend you flashing it. You can always flash back (make a backup before though), there's a copy of it and instructions on how to do it in the documentation.
Cheers!