Hey, just started playing today. I'm gonna try and record my full gameplay for YouTube over the next few months because this looks pretty sweet. Noticed you wanted any bugs listed that a player notices, not sure if these are specifically New Threat problems or were always in FF7, but I'll try to keep a running tab of everything I see. I can provide links to direct video if you'd like (though some clips won't show the specific problem, I can at least use it to reference for you).
After freeing Jessie's leg in Sector 8 escape and after the Scorpion fight, she just floated up the ladder exiting the room. When I replayed it, she didn't do it, so I'm not sure what triggered that, but there was no climbing animation up the ladder.
During the Sector 5 meeting in the basement of Seventh Heaven, after Tifa descends, Wedge's "talk" area is pretty huge. I was trying to use the pinball machine to leave but he was still saying "Ah, well look who wants a friend."
The boy in the white shirt in Sector 7 repeats his old lines after his new ones. He'll say something about "Explosions! AVALANCHE is so cool!" and after you trigger his new dialogue, he'll follow up his "I got no one to pick on" line about Johnny with "Explosions! AVALANCHE is so cool!" Leaving again and talking to him a third time he'll say how he's a coward or something, he's got no one to pick on, and explosions!
This is awesome, though. I really like it. 7 is not my favourite Final Fantasy game or even 2nd favourite, but what changes you've made so far have made the dialogue and story way more interesting to me.