In the original FF7 draft, Wutai was a bit different with additional characters. Sera was a sort of possibly-undercover Shinra propagandist that was overseeing an intense tax on Wutai or something to that effect.
Himemiko was a young girl that was Wutai's princess and in line for the throne. I think her guardian was Lady Izayoi? Something like that. There were different scenarios around them. It was much more of an occupied territory sort of story. If we're getting more Wutai NPCs, I hope they return to these cut ideas.
I think Yuffie still steals the materia, but there will be more set up and drama to it since she's no longer optional. They've kept her materia obsession in the Remake, so its still a good way to make use of it, especially with the "Ultimate Materia" not yet complete.
I think it's unlikely they will revert to ideas they had in the original draft. They've moved a long way away from those early concepts, and they probably wouldn't fit with whatever they have in mind for the Remake.
What Yuffie disrespects about her dad was that he surrendered to Shinra in the first place. And turned Shinra into a tourist location. If anyone is the Shinra Agent in Wutai, it's probably Godo TBH. He *wants* there to be no more fighting with Shinra. The Five Gods of Wutai in the OG all seem to at least know of his motives and don't fight him over them as well. They seem to be more worried that Yuffie won't understand his motives since she's a kid and the situation is a lot more complicated than she likes to think it is.
But they mention in Intermission that he's in prison, how can he be a Shinra Agent? Clearly there is a shift in the story and a difference from the OG. We'll have to wait for the Wutai part to kick in to know more about it.
Maybe it's the Wutaians holding him in prison.
I mean, we don't know, but if he was the one advocating for peace with Shinra - a la Barret in Corel - it wouldn't be beyond the bounds of possibility for Shinra to betray him as part of the ceasefire agreement and hand him over to some new government in Wutai for punishment. Once he was no longer of any use to them.