I think, VCCA is more critical and should be decoupled from general supply. Instead of a VCCA island, which is typically unwanted with limited power planes, individual bypass caps and ferrite beads for all four VCCA pins should be considered.
Generally, due to the internal PLL voltage regulators, Cyclone III is considerably less susceptible to PLL supply voltage intefernces than Cyclone II. I guess, that you most likely won't have problems when connecting VCCA to common 2V5 node with good decoupling, but I didn't try and thus won't suggest it.
In contrast, I have VCCD tied to VCCINT in all Cyclone III designs and didn't yet experience PLL lock problems. For lowest jitter, separate VCCD decoupling may be still useful.