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im going to be programming the fpga using a micro controller when the board boots up, so no need for JTAG. although would you recommend having a header any way just incase?
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The JTAG interface is;
1) A programmer
2) A communications interface
3) A logic analyzer interface
4) A NIOS processor debugger interface
5) A custom JTAG interface
.... and many more
The passive serial interface is *only* a programmer interface. You need it to program you device at power on. The JTAG interface is for all the problems you haven't thought of yet :)
Cheers,
Dave