Hey Sega Chief,
You mention being wary of wanting to add stuff that comes across as fan-fiction, but some of the best aspects of New Threat I thought were the added dialogues, such as talking to the party members in towns. The Dark Cave quest I also thought was fantastic, and I wish there was more like it in the game.
I understand your concern about conserving the "purity" of the game, but I think that as long as you don't mess with the main story, no one would complain. I think you have a knack for writing and designing cool scenarios, and I think it would be to everyone's benefit if you let your creativity run a little wilder. I think relegating these scenarios to optional endgame sidequests is perfect.
I'm aware that 2.0 is the final version of your mod before you move on to FF8. I'm taking the time to mention it in case you ever work on FF7 NT again in the future after the release of Sister Ray, and also because I'm hoping that you let your creativity flow for FF8 NT.
Cheers