I would compare the wireless specifications between the fios's router against the AE and then go compare the actual wireless range for both in your house. You might find one has further reach than the other or worse that you might need both to fully cover your house. The AE will provide other apple centric features that fios router won't provide, just to name a few: time machine server, file server, Back-to-my-mac, bonjour services, print server and probably a few more.
My impression with the supplied fios's router was rather positive initially, it's probably the best parental control router i've seen. My positive experienced turned sour when i noticed one day that my wireless devices could no longer see the wired portion of the network, turns out your ISP will update the firmware, something you won't have control over, and the firmware installed had known bugs with the issue I experienced. Since you can use your own router, I just picked up an AE and never looked back.