There was nothing in the game lore to suggest yahgs or thermal clips, either - at least until the writers added them. This still doesn't seem like a very good reason. It's entirely likely that they come up with a terrific reason and means.
It's also not out of the question that they resort to some sort deus-ex-machina either, but honestly, if it's just a way to kick it off, that's not an insurmountable obstacle. The only other way to deal with it would be to take a time machine back to pre-ME2 and fix the nonsense hole they wrote themselves into.
Yahg are not an unreasonable addition. There are likely numerous pre-spaceflight races out there. One being the Shadow Broker is more of a stretch, but not an insurmountable one.
The thermals clips was just plain stupid. And yes, Bioware was called on it. Repeatedly. And their response was...to lampshade it in a conversation with Conrad Verner 
Well, at least ME3 had a couple of weapons with overheat mechanics we could use.
As I said, I have no confidence it will be explained in any satisfactory way. No doubt we will find yet another long-lost artifact. Or perhaps "RESOURCES!" will allow for this miraculous new technology to be built. Or hell, maybe it'll run on organic energy. Or something.
Time travel may well end up being the more plausible answer.
Basically why should I get invested in a world or setting when its foundation is made of sand?