Why was Episode Two green-lighted to begin with?
You mean "The Naked Now"? I think it was partly because the premise was a good way to develop the characters. ...
Plus I think they wanted to do one big nod to the original series before moving on.
From the first airing in '87, I always saw the dialog as Wesley implements his reverse-tractor beam as a blatant disclaimer about the aim of the show from there on:
WESLEY: ...Repulser beam hard against Tsiolkovsky. Don't you see? It's giving us a push off. The extra time we need.
RIKER: We're pushing away.
While being an exact replica of a TOS episode, it ends with them "pushing away" from a TOS-era ship and going off on their own path.
Whether or not it was actually intentional, it always has been so in my mind!
That's a remarkable metaphor! Wow, I never thought of it that way, but I think it's an cool observation.
I was probably too distracted by the fact that when Wes says to use the tractor as a repulsor beam that everyone thinks it's brilliant when on TOS all Sulu needed to do was change the setting, they always could do that. Maybe it's lost knowledge that you could do that by the 24th century.