While I'm not sure what people desire with a "Wutai war game", my intuition is that any outbreak of actual conflict (that the players personally witness and participate in) will be brief.
In Part 1, a running red thread was the Whispers and this was "paid off" with the battle against the Whisper Harbinger.
With the Whispers no longer active agents, I expect Part 2 to choose a different red thread which will pay off with a Big McLarge Huge boss battle at the end. The red thread I see being the ready-to-explode political situation between Avalanche cells, Shinra, Wutai and our main protagonists.
Cloud & team will follow Sephiroth around the world, but they will also encounter Avalanche cells along the way and we'll get to see multiple perspectives on what is currently happening at Avalanche HQ, Wutai and with Shinra. We might also see some timeline fuckery (alternate universes bleeding into each other or what have you) but I see that being a mystery to be left until at least you get to the Temple of the Ancients.
I take mostly at face value what Biggs said about Avalanche HQ promising Wutai all the materia in Midgar. Although Biggs words it as a deal that has been made, I reckon the leader of Wutai, Godo, has not fully agreed to anything yet. Avalanche HQ has presented an offer that Godo has not yet accepted, but they expect that once the materia is delivered, Godo may be motivated to accept the deal.
My speculation remains that Avalanche HQ wants war to arise between Wutai and Shinra, since a war where Wutai wins may lead to the mako reactors being dismantled. The reason Avalanche HQ deemed Barret's cell too extreme is because Barret's actions might kick off a war too early, before Avalanche HQ has stolen enough materia for Wutai. Indeed, FFVIIR Part 1 showed us how Shinra took advantage of the situation and were on the cusp of using a conspiracy to start war with Wutai.
Had President Shinra remained alive, war would have started pretty gosh darn soon. Rufus Shinra will slow down these developments, much to Heidegger's frustration, if only because Rufus still needs to determine if they can come out of this conflict with enough profit.
One way to have this end with a Big McLarge Huge boss battle is if another rogue Avalanche cell ends up summoning Zirconiade. I don't necessarily like the idea, but it'd be simple enough to declare in FFVIIR canon that Zirconiade has never been summoned yet and instead move its summoning to FFVIIR.
Part 2 might then end in Wutai, where we see the climax of the Wutai/Avalanche vs Shinra war plot but ultimately have it defused by convenient plot points (such as a rogue Avalanche cell summoning Zirconiade). The plot will then remind us that Sephiroth is still a threat and that we need to find the Black Materia.
Not the most beautiful outline but I can see them doing some interesting stuff with this. I look forward to seeing how Yuffie will play into all this and how they might change her events to fit the new plot.
