The Cyclone® III Device Family Pin Connection Guidelines (PDF) version 1.0 provides the following pin connection guideline for GNDA:
"The designer should connect these pins to an isolated analog ground plane on the board."
This recommendation is based on a low cost board design where there may only be one ground plane. In such a design, the ground plane may be subject to excessive noise from the switching activity of all of the devices on the board referencing that plane. Thus, Altera recommends providing an isolated ground plane for the PLL analog ground pins.
When a board is designed with multiple common ground layers, the ground planes should be quieter compared to a board with a single ground plane. Although this requires additional cost, it does allow for a more robust power distribution network. When the ground network of the board is designed to be as quiet as possible, it is better to connect GNDA directly to the common board ground reference without any need for isolation.