Issue 10001984, Version 3.1
Stratix® II GX Pin Connection Guidelines recommends using an isolated ground plane for the GNDA_PLL pins. This recommendation is not necessary. In general, it is good practice to have a common ground. In the case of Stratix II GX devices, there is a common ground inside the package. Isolating the GNDA_PLL pins on the board would not serve any purpose.
This recommendation will be removed in the next revision of the Stratix II GX Pin Connection Guidelines.