As for the compile times, I think they'd be about the same. For Java, I know they are using the standard java se compiler, and the compiled code will be uploaded somehow (not FTP anymore).
For the boot times, I'm hoping they'll be faster.
Linux can boot really really fast. I've got a little device that runs an FTP server at my house that boots in < 10 seconds.
I know that it will take a little longer as it needs to load the FPGA image/network stuff/user code initialization, but there isn't a reason it needs to be slow.
Check this out
http://www.youtube.com/watch?v=-l_DSZe8_F8