Destroyers should be built less along the design of the Orion and more along the design of the Hecate: non-direct combat platform. Everyone says the Hecate sucks because the Orion easily outguns it with beams. The Hecate holds more fighters, and those fighters and bombers can easily vaporize an Orion (see NTD Vindicator) The last place these destroyers should be is the front line. A Destroyer should never be alone. It should have a 'battlegroup' formation it travels with.
Build more Deimos corvettes and upgraded Aeolus as well as Sobeks. The Colossus should never be built again. It was big, it was expensive, it housed

of people, and Alpha 1 killed more ships than the Colossus did in the campaign. Fast, tough, and versatile should be the motto of new ship design. I think the Deimos should keep the Slash beams... they are awesome at taking out turret hardpoints, but maybe have 1 BGreen on it.
Scrap all Fenris and Leviathan cruisers.. they are totally useless and are glorified coffins for the people in them.
Mass produce Helios bombs.
Build a Knossos device.
But maybe the Shivans wont return.. perhaps it was Bosch's intervention that stopped the Juggernaut fleet from raping the GTVA completely. Or it could be that the Shivans do not intend to wipe out humanity. I think this war brought the GTVA off its arrogant pedestal it had sat on when it built the Colossus.