You can't, directly, compare a discrete processor solution versus a softcore processor in FPGA (like Nios II).
Yes, Nios II is not likely to beat a desktop processor, cycle for cycle, but it's possible for a Nios II based system to outperform a desktop system....for certain applications. This can happen with RTL-based hardware acceleration (C2H, etc.) or DSP-based acceleration, both of which are possible in Nios II (in FPGA) systems.
Your job will be to determine if a Nios II system can compete with whatever discrete processor system you have in mind.
Best Regards,
- slacker