The GTVA has a number of issues facing them at that point in time.
Reduced naval strength, both literally (losses in Capella) and figuratively (obviously no longer believe themselves capable of handling a Shivan incursion).
Heavily industrialized/populated systems formerly controlled by the NTF: possibly in need of reconstruction (though the speed with which the NTF collapsed makes this somewhat unlikely) and with shaky loyalty.
Loss of Capella (physical resources)
Capellan and other refugees.
Of these, only one cuts to the core, threatening the survival of the GTVA and the Terran and Vasudan species. The losses they took in Capella can be rebuilt, so can factories. People can be resettled. Loyalties can be changed. Even new systems can be settled to replace Capella.
But the GTVA does not have the ability to confront the Sathanas fleet on anything within yelling distance of equal terms using the weapons and ships they have available. To build up to the force levels required just to face a significant fraction of the Sathanas fleet would take decades. It isn't just building the ships and training the crews, but building the infrastructure to support them, the shipyards and the factories and the academies. The GTVA's economy probably can't support the kind of effort needed to reach even that minimal capablity to deal with the juggernaut fleet, at least without restructuring. This would be the work of a half-century, easily.
And when numbers will not serve, something else must. Tactics, technology, quality. The GTVA can be expected to rush ships and weapons designed to deal with juggernauts out the door within seven years of Capella, probably even within five. There will be great emphasis on doing more with less. We must remember that the GTVA fleet we saw in FS2 was essentially the product of a peacetime military. The ships and fighters were designed before the NTF Rebellion. We are likely to see a great number of stripped-down designs surface, ships meant to do the same jobs just as well as the old ones, but do them at lesser cost using fewer people. The GTVA is likely to totally rethink their tactical and strategic doctrine.