You can reduce file system internal fragmentation by using a smaller block size in your VFAT format. You can do this with the "-S" option of mkfs.vfat. I use a block size of 512 bytes.

If you are serious about cramming as many maps into your card as possible, you should use ext2 and use hard links to represent map tiles that are "the same data" - water maps are all solid blue, so you can save the additional 103 bytes per tile.

Other map storage mechanisms have been considered and discarded in favor of the RAM and CPU efficiency of using the file system (including adding and removing maps on-the-fly).