Norbert, you're oblivious to the fact that PVE never had any unique weapons beyond Vasudan Light Laser. Yes, they used same primaries and secondaries as GTA before, on and after the Great War. And so did Shivans use same secondaries and their weakened versions. Your point about Avenger, Tsunami and whatever is thus completely moot. Volition simply did not give them any unique weapons besides Vasudan Light Laser.
As for which one was going to get upper hand. I would say neither. The war had already progressed to a point where both sides had more to lose than win by continuing full scale war. Both had sustained major losses throughout the years and financing the war was becoming a problem. If Shivans had not appeared when they did, I would assume the war would have turned into smaller skirmishes and eventually cease-fire would've been signed.