You bring up some good points eleazar. Like I said it was just an openeing draft but I guess I might develop some answers for you.
Who is the "unknown force"? Yeah you wouldn't tell the player right off, but these guys seem like they should show up again somewhere.
I guess I left this part fairly open. My original concept would be a group of religious extremists, composed from each of the precursor races but controlled by an outer force, something toying with the precursors just as they toy with the player races. This higher entity's motivation would have been the prevention of the Engine's use in order for it not to reveal the power's identity to the precursors.
But it would be better perhaps if this was a random element to the plot revealed only through strong end game ties to a precursor race or through recovery (but not operation) of the Engine on Orion. One result could be the one above, another could be a random one of the precursors who never got over their old rivalries. Or a more 'out there' possibilty could have been the Engine itself interfering with the past once it is activated in the future by one of the player races, its motivation would have been the Engine's view of the precursors, after all they nearly destroyed the galaxy.
If the powers are so wiped out that they can't fight any more, how do they have enough resources to start over in a new galaxy?
They weren't quite wiped out, after a century of violence they had begun to lose resources (and planets to recover them from) and they knew if they were to continue down their path then there wouldn't be enough for them to fight over.
If they have the ability to leave the galaxy why haven't they done it before
At the time their most ideological goal was completion of the Engine and therefore everything else seemed to take a back seat .Like the real world mission to Mars idea, JFK wanted it by 2000, but at the moment it's scheduled for 2050. And an intergalactic journey is big no matter who you are, the Star Lane network probably took centuries to construct.
Besides without Star Lanes, any journey is exponentialy longer, therfore even with ships equipped for the journey, the Exodus would have taken thousands of years.
If the engine wasn't totally busted, why didn't they try to fix it, or in total-war mode why didn't someone blow it up to keep it out of somebody else's hands?
Remember that everyone who ever worked on the Engine was brutally murdered, they were all the greatest thinkers in galaxy so therefore it would have taken far longer to fix it even in peacetime. As for blowing it up, after so many years working on it, the Engine even in its damaged state was too important to destroy completely, if anything they might have tried to relocate the Engine, but if they tried, they didn't succeed, it would have been hard with all five races fighting in Orion's system anyway
Of course that doesn't mean one or two of the precursor races might have changed their minds about it in their millions of years in isolation.
If the engine is so busted that the precursors can't easily fix it, what value does it have to player species?
Whether they could fix it or not, the Engine is a very valuable bargaining tool for players with the precursors.
You haven't given the precursors any motivation to do anything expect take back the engine, and try to fix it.
Well these races are supposed to be the same five you came up with. Their isolation would have changed them into the Unifiers, Engineers, Observers, Caretakers and Final Ones. Not to mention the galaxy used to belong to them so they would want it remolded into anything they wanted.