I'm not sure what kind of limitation you think there is.
1 or 2 Mbytes might refer to the number of address lines of the mini-flexbus interface. It has nothing to do with USB.
2 Gbytes might refer to some kind of limitation of the FAT filesystem. Again, it's not about USB itself. You can choose any filesystem, or work with none at all. That's a design choice, it's yours to make.
There is no fundamental limitation of the maximum size of a USB flash drive. It should be possible to use all of it.