There's no comparison (well, there's some comparison). Nios is more akin to a microcontroller while the Arm processors in the SoC devices are applications class processors. Nios works well with no OS or an RTOS while the Arm processors work great with a full OS like a Linux variant and aren't suited well for an RTOS.
You are right. Perhaps I should have been more clear.I did mention ARM cores, instead of processors, because many popular microcontrollers are based on those (eg NXP Kinetis, Atmel SAM etc). So, from a speed point of view, would it be better to implement a NIOS II in a MAX10 or just add an Atmel SAM3X8E on its side?
If you need just more performance just go with fpga with arm integrated, no hassle with high speed signal integrity issue between cpld and ic that could be a bottleneck.Arm core is more optimized than nios but more complex