The Unbidden fleet power is MASSIVELY overrated. They are mainly using shield and energy weapons - use torpedoes (which ignore shields), hellfire guns (which have such a fire rate they prevent shields from regenerating), coilgun/artillery (which ignore a good part of shield and armor) and disruptor (doing massive shield damage) and you can really tear through their armies. Protect yourself with shields (their weapons ignore armor IIRC, so shields are better).
I managed to annihilate about 600-800k of their forces with 100-150k of mine, losing about half my ships in the process. I can rebuild my forces far faster than they get reinforcements, and I actually feel so barely threatened by them that I let them expand so they eat my competitors, and I even started a war against the FE they have battered for a while - that's how easy they are to counter.
The teal empire, the leftmost arm of the galaxy and a good chunk of the inner right arm (right above the double-eagle) were part of the Sakyt Arbitrator just before the latest war, where I nabbed a good chunk of their territory and released the teal empire (the Sakyt Arbitrator and the blue circle inside their borders, are both awakened FE). I was much more afraid of them (they had just as much territory as me, and had a large advance in both technology and fleet power), but they seemingly had bad ship design, as they lost most of their forces to the Unbidden. I thought it was better to stop the Unbidden before they became unstoppable, so I sent all my fleet to fight them, but after the battle described above, I realized they just weren't that dangerous if I used the right weapons, so I went back to capitalize on the opportunity to have them push through the FE on one side
(and yes, I use a mod to remove sector limits. I just find them annoying and frustrating, and it makes the game boring because there is nothing to do)
The Prethoryn are their opposite : lots of armor and missile weapons. Just use arc weapons (which ignore armors), tons of Point Defense/Flak, and lots of armor (I'm not sure, but I think their weapons do raw damage, so armor actually reduces it a ton). You'll probably be able to tear through them even more than the Unbidden, as you can actually destroy their offensive power before it reaches you.