Unfortunately there isn't going to be much you can do to speed up the bootup time of the VxWorks OS running on the real-time controller of the CompactRIO. I suppose limiting the software installed on the controller will help but not to the levels you're looking for.
Depending on your application, one thing you can look into is using a custom FPGA VI that is loaded and run on the bootup of the CompactRIO. The FPGA VI can't immediately require any input from the RT host VI but it will get an application running much quicker after power up than the RT host. If you're interested in this method, some information about enabling the behavior can be found at http://digital.ni.com/public.nsf/allkb/BC513C2A0DC29C89862574BF0002B0B9?OpenDocument.
Let us know if there is anything more we can help with.
Alex Person NI-RIO Product Support Engineer National Instruments