The original games weren't NES games. Faxanadu is a famicom-themed spinoff of Xanadu, which itself is a sequel to Dragon Slayer. Dragon Slayer and Xanadu are much more popular than the famicom spin-off.
It's also more accurate to say Zelda II is like Xanadu, than that Fauxanadu is like Zelda II, considering Xanadu predates Zelda II. The true progression would probably be something like this:
Zelda 1 -> Maze of Galious (Konami) -> Xanadu (Falcom) -> Fauxanadu
As Xanadu is clearly inspired by Maze of Galious, which itself was essentially a side scrolling Zelda title, and Fauxanadu is a pretty logical evolution of Xanadu.
It all comes back around with Xanadu 2, which is basically a Zelda III clone.
That certainly hasn't been my experience. Also, I didn't say Faxanadu was a Zelda II clone, just that one might enjoy Faxanadu if one enjoyed Zelda II. I didn't know what system Faxanadu's predecessors were for, though.