People say the Colossus was designed to fight the last war as a criticism, but what should Command have done if they knew what the coming Shivan fleet would look like? It was designed to be as powerful as they could possibly make it, it's not like they got to the level where they thought they could beat the Lucifer and designed to stop there.
All you can really do against a Sathanas fleet is what they did - load up some destroyers with explosives and take the relevant jump nodes out. Having the Colossus didn't stop them from doing that, indeed if you buy what the Colossus said in Their Finest Hour they actually bought time for that strategy to be used effectively.
One mistake I would say Command made is having the Bastion travel from Capella to Epsilon Pegasi rather than having a ship depart from Epsilon Pegasi to Capella. Maybe the Meson Bomb production facility was in Capella.
