I second the op's questions. This game does indeed have a plot. Otherwise, how would these questions arise in the first place?

I think you're confused about what a plot hole is.  A plot hole is an inconsistency or irregularity within the plot that has no real explanation except author oversight.  What you're describing are certainly not oversights, merely information that was never given in the first place. 

As for whether we'll see the answers or not, probably not any time soon.  I actually think one of the magical things about the Sins canon is how ambiguous and open to interpretation it is.

From what I remember reading, the Vasari didn't create whatever is chasing them. They used technology that was in existance long before their empire ever existed. Who left this technology just laying around all over the universe (almost like they wanted other races to use it) nobody knows. The Vasari attempted to study the technology to understand more about it, and in doing so started whatever it is wiping them out. Whether it is the original race that created the jump phase technology being released by the Vasari from another universe/dimension is a theory I currently hold. Regardless, I don't believe the Vasari created whatever is chasing them....they just released it.

I don't think what is chasing the Vasari creating phase jumping, or at least the other races discovered it independently. Otherwise the TEC and Advent couldn't possibly have had it before the Vasari appeared, and it seems that it was known to them for at least 1,000 years as how else would the TEC have gotten tot he Advent homeworld anyways?

As to what is actually chasing them, I think it is some other super advanced race (or perhaps machines?) that they were unfortunate enough to discover while expanding their once mighty empire. However, it seems the Vasari aren't completely outmatched against them, as it has been what, 25 years since they first appeared by diplomacy, so they must at least have better phase jump technology. I don't think it is Nanotech, and technically we don't know if the Dark fleet managed to do any damage or not, all we know is that one ship survived. They could have taken out half of the enemy fleet they faced for all that we know. I would be willing to bet however that they appear in whatever is next for Sins.

Also, Trader Defense Navy FTW!

Of course all the races had the phase jump technology. It was spread around the galaxy before the Vasari even found it. I'm not sure where I got all this info. I think it may have been in the game manual. I'll see if I can find it.

Correct. Phase Jump Inhibitors have been around since before the Vasari; the Vasari don't even know how PJI's work, they just know that they work and that they can be successfully replicated with nanotechnology.

Because PJIs predate the Vasari Empire, it's plausible to conclude that whatever created the PJI's may not have had Phase Drive technology, but was fighting a foe that did; thus, to prevent the foe from disengaging at will, this race created PJIs.

It's also quite possible that PJIs are why the Dark Fleet was virtually destroyed. After all, in-game at least, the Vasari require either a Marauder with Distort Gravity or they destroy the PJI to escape its influence.

"I don't grin like a moron, I grin like a sociopath."

The fact that Vasari would rather fight their way through a 1.18 battleball is evidence of just how terrifying their foe is...

They were indeed left behind by some ancient civilization, on that we can agree, but on the back cover it says:

"Assume ultimate control over one of three galactic powers: and ancient alien civilization running from a terror of their own creation, a loose coalition of traders forced to annex their own people, or an exiled empire of powerful psionics bent on revenge"

terror of their own creation means to me that they...umm...created it.  And nanites are the vasari's favorite technology.  It could be that they made some experimental type that went nuts and attacked everything in sight.  The vasari we play as have never actually seen the thing chasing them, which explains why they still use nano-technology.  Ignorance is bliss.

-Twilight Storm

Nanites come to SOASE galaxy

TEC/Advent/or Vasari Come up with a way to neutralize Individual Nanites, so the cloud forms into ships.

You could even have Nanite Clouds out there as a new Neutral Grav Well that hurts your ships until you research the counter to it.

That's just one way to makeit work.

But I do see your point, it doesn't necessarily HAVE to be something they actually made.  I just think that's the way it reads.

-Twilight torm

Its lemony fresh, LOL

I've got my own backstory that I've been thinking up for the vassari and the "darkness".  But I never thought about the PJI's.  Hmmmm... I'm gonna have to write and brainstorm some more....

I like your theory, though one thing kind of bothered me about it. The nanites may have gotten out of control, but would they really be determined enough to chase the remaining Vasari through space?

I don't think that nanites perpetually chasing the Vasari seems very probable unless there is something controlling them. I would think that the nanites are rather nondiscriminatory left to their own tendencies.

If they are nanites, I think that there must be some kind revenge/hate plot with a member of a conquered race that somehow is able to control them.

I think the Diplomacy expansion makes it clear as to who exactly chased the Vasari off - the PIRATES