How to make the uclinux boot faster?

If you are seeing the "Uncompressing Linux" or the beginning as it appears to be than it seems like it is still the compressed version. For my system the uncompressed kernel is located at "uClinux-dist/linux-2.6.x/vmlinux". I would try to use "nios2-download -g vmlinux" and see if that works with the file first before starting to rewrite flash. You can see the code that prints out that line in "uClinux-dist/../linux-2.6.x/arch/nios2/boot/compressed/misc.c"

The bootloader provided by Altera doesn't actually decompress anything. The CFI bootloader just starts copying the data from flash to the correct locations in RAM based on a simple header where the first 4 bytes indicate the size to copy (if 0 then this is a jump record, if 0xFFFFFFFF then a halt record since the flash is probably erased), the next 4 are the address to copy or jump to, followed by the data. This process is described in App Note: 458 http://www.altera.com/literature/an/an458.pdf