I have done several videos on the MiSTer FPGA project, where I connect cartridges to the unit via USB. Now, I am aware that the cartridge is dumped to memory and then read, but only after the first time. Now, I framed it as a “Build Your Own Polymega.” It is a similar idea.
One of the things I. noticed with the USB-NES (now opened sourced) was that the Retro-bit version of Metal Storm was incompatible. I contacted the developer and we worked together for a few tests and he came up with a solution, which I demonstrated here:
I’ve only noticed this with the Retro-Bit cartridge, but it needs to be in just the right spot in the USB-NES. I checked the hash of the ROM each time I moved the cartridge around. When it changed, I tried the cartridge on the MiSTer and that is when it worked. I even got credit from the USB-NES developer in his GitHub.
I know there are newer options for the NES now, but I have had an excellent experience with this.