Isolation filter for VCCA in Cyclone-IV E

You'll find different suggestions in different Altera documents. Since ever, either ferrite beads or low value resistors have been suggested for filtering of sensitive pins, e.g. PLL analog supplies. On the other side, you'll notice that many development kits are tying VCCA to the general vcc25 IO voltage without additional filtering. You can read this in a way that the IO voltage is achieving sufficient low ripple (e.g. < 0.3 V as required in the CV pin connection document) without additional filtering, which sounds plausible.

I use to keep a 600 ohm/1A ferrite bead for VCCA. This might be a reminiscence to Cyclone and Cyclone II FPGAs that didn't have internal PLL voltage regulators and were rather susceptible to supply voltage ripple, resulting in PLL loss of lock. Cyclone III and above are hand-tame compared to it.