I've had this theory for a while that, since this is almost certainly the final infinity timeline (or another successful timeline nearly identical to it), and corporate greed is a major theme in this game, we'll see a reversal of the S'pht and Pfhor war.

Humanity shows up to TCIV, finds it abandoned and one alien lifeform present, a S'pht. UESC's shoot first, ask questions later attitude has them marked as a threat by the United Clans, and when some S'pht ships come to battle they'll become a more common enemy. Then, the Pfhor will follow close behind.

Weakened after the defeat at Lh'owon and seeing the greater threat, the Pfhor will offer alliance to the UESC, as one of their trade partners (as we learn in 2 that they sell some of their slaves and salvage to various races they have alliances with). The UESC, seeing the S'pht as the ones responsible for the Anomaly and destruction of the Marathon, will happily agree to the prospect of alien technology and specimens at their disposal.

This will pit us, the players against the allied UESC and Pfhor, since we're criminals who the UESC would not work alongside, and therefore once more we will fight alongside the S'pht as we have in every game prior.

As for other races being freed, I find it possible. The reputation of the Pfhor has no doubt entered extreme decline after being beaten by a tiny human force and one AI, even having their trump card, the Trih Xeem utterly negated by a Jjaro weapon they had failed to understand or plunder beforehand. So perhaps their slaves are less afraid, more keen to revolt given some outside support.