I keep reading about the fuss because some of the ships and technology is nearly the same.

Well I may have an answer for you all. First mankind no matter if they are deviant or Tech will have similar technology to a certain point, the Unity of Cyber humans have deviated from the normal and  invested more into mind altering firmware augmentation including wetware according to their beliefs, the Colition saw this as abhorrant , still no matter how advance their psi cyber tech is, their ships should not be too different from the Col.

The aliens, well this is where it can be different but only to a certain extent because these freaks are on the run from someone more powerful and deadly, however because they are on the run then it is possible that a lot of their technology may and I repeat this, may have been lost over time, I mean think about it, if you are an advance civ but was getting your butt kicked until you was on the run then  it would only stand to  reason that you would only be able to carry only so much of your tech with you, logic says that given time you would stagnate so now your advance ships may not be all of that and a bag of chips and the next race that you may encounter may not be that far behind you and who knows according to the game mankind will sooner or later stumble across some of that tech and so leveling the playing field.

Of course this is only a what if and it is up to Ironclad to flesh out the story in a nail biting campaign