Oh ye of little tech room reading!
The victory over the Lucifer had dealt the decisive blow. Incapable of coordinated strikes or strategic planning, the Shivans were outmaneuvered, isolated, and gradually destroyed. However, both species faced the challenge of rebuilding their interstellar societies from the ground up.
Ah, Reconstruction article.
To be fair, the combination of the sudden loss of a probably thousands-year old nigh-invincible superweapon that they had probably gotten quite comfortable having around and the loss of experienced command personnel aboard would probably draw a huge 'oh crap, what do we do now' reaction from any civilization.
Being the biggest fish in the pond, by far, for thousands of years(likely more) with no one to give you any real fight would probably result in a certain complacency and strategic/tactical sterility; alway knowing that if things really go south, you can always just point the Lucifer at it and call it a day; knowing you can break the back of any concerted assault against you without breaking a sweat. More importantly, not only that, but knowing that your enemy knows that(thus greatly limiting the scale of their operations against you), and never having lived in an environment where that wasn't the case(assuming Shivans have reasonable life spans, anyway).
I mean, did anyone really feel the Shivans would have gotten anywhere near as far without their superweapon? Before it appeared, we were getting even so bold as to disable an entire live cruiser of theirs and just cart it home for study. Command sent three wings of fighters/bombers to kill the undamaged, "full armed" Eva destroyer(okay, Alpha 1 was there, too, so add the equivalent of another couple of wings).
If the game is supposed to be any indication, the combined Terran and Vasudan fleets, after acquiring the Shivans' shield technology, and developing the Tsunami and 'modern' fighters(Hercs, Ulysses) and bombers(to say nothing of the Ursa/Harbinger), would have slowly, but absolutely surely, chewed our way through a Lucifer-less Shivan fleet with all the resources we'd have not lost from being shredded by the Lucifer itself(Tombaugh, probably most of the Vasudan fleet, etc).
(Of course by my thinking, without the Lucifer, they'd have been forced to come up with new technologies and tactics, but that delves even further into the realm of pure conjecture...)