NIOS II Power and Heat management

Your approach sounds good. With ~12 CPUs I can see why you are looking into this.

http://www.altera.com/literature/hb/qts/qt...ts_qii51016.pdf (http://www.altera.com/literature/hb/qts/qts_qii51016.pdf)

That document has some power saving techniques for Stratix II and I'm sure most can be used for Statix as well. If this was me trying this I'd probably put each Nios II core into its own SOPC Builder instance and try to use the clock control logic Quartus II has (it's probably describbed in that link).

Good-luck