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This is the situation with combining BC and NT:
Both affect event scripting and dialogue, and the automation tools we have aren't able to discern what is a critical script and what isn't. That means we have to take a field's script in its entirety when combining mods. So that would mean some fields would be using only BC scripts, and others would only be using NT scripts; besides the technical problems that could cause with mis-matched variables, etc. it would also be an incomplete experience of both mods.
Same goes with dialogue; even if we took all the BC text and ported it in, some of it would be mismatched due to NT's custom field scripting and a lot of the item pickups would likely display the wrong item (as these are unfortunately written as regular field text and not retrieved by the game based on the acquired item's ID).
However, all that only applies to automation. The process can be done manually and could probably be done so that both mods work seamlessly together given a tweak here and there. Best approach is to take the BC mod as a base then apply the NT scripts onto it; I'd likely be the best bet for that because I know where most of my scripts are and how they behave (plus it'd give me a chance to clean the older ones a bit and make them tidy).
So here's an idea; I was going to make a NT 2.0 after I was done with FF8 NT's Disc 1. What I could do instead is use a finished BC as a base for that and kill two birds with one stone. I'd also be able to set up the NT text in such a way that porting between BC and NT dialogue can be done without issues via touphscript to avoid issues with wrong text/out of context dialogue.
As for right now, you'll need to decide to either wait on that (could be months), or to play BC or NT. NT does have a text overhaul but it's not based on the Japanese or anything (though I referred to the translation whenever I hit a scene that I was struggling with).
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If the top menu froze ATB, then you would be essentially forced to act with that character in order to get it moving again. When playing I'll sometimes delay on a turn to let an enemy act and see what he's going to do while letting the other character's gauges fill up.
There does seem to be inconsistency with certain cast animations though. I think it can happen with Limits that it keeps running under certain conditions but I'm not sure what the exact circumstances were; it might be different for each animation file if the game locks/unlocks ATB based on what animation frame its on.
I think the countdown timers go slower on slow speeds but faster on fast speeds so adjusting the ATB speed would probably work against you in that case. Gauge speed is a potential problem when paired with ATB behaviour because it can make status effects resolve too quickly; this is particularly problematic when Barriers are being taken into account with balancing.
Didn't really see the wait trick as too big a deal. Its benefit depends mostly on speed differences and it's mostly only used in speedruns or challenge runs where the mechanics need to be pushed and the fights tightly controlled.
FF7 could benefit more from such a patch than FF6 due to the longer attack animations, but it's not my preference. I found it made things restrictive and clunky when I was going through BNW's ATB patch; in my mind balance is fine so long as it doesn't impede the fun or the flow. I don't want to sit and wait on every single animation, I want things to be moving along.
If such a hack does come up though then it'll (probably) be compatible with NT out of the box as the game is split into separate files unlike a ROM. I'll ask people about it on discord and see if they know more about the inner workings of the ATB system.