Whether he intended it or not, it was still basically the same plot, just done better. Hell, the V'Ger plot was once going to be used as the pilot for Star Trek: Phase II, if I recall correctly.

EDIT: What freaked me out about that episode was what happened with Uhura. The damn thing wiped her entire brain... yet they're able to re-educate her?! Were they able to re-educate all her memories and feelings and instincts? Or is the Uhura we see from that point on basically a whole new person?