I think the primary failure of the Federated Commonwealth came from a rushed integration and a failure politically to sell the changes being made on the ground. A lot of sources from the FedCom era paint a picture of AFFS officers being assigned to Lyran units and essentially saying "it's cute that you chaps think you're a military, but I'm going to have to show you how to run things proper". Lyran military practices, even ones that worked like lightning companies, were never adopted in the FedSuns and were washed away in the rush to mimick the AFFS as closely as possible. The combination of this with Hanse's political domination of Melissa is what I think leads many fans to think FedCom=FedSuns.
On the flipside, for the entirety of the true FedCom era, Suns military industry was basically sidelined in favor of the Lyran half. Considering the Clan invasion, you would think it would have been wise to expand Davion factory production, but oh-no! While all the Federated Suns brought to the table was the Caesar, Penetrator and a bunch of clunkers (Watchman! Fireball!), meanwhile, the Lyrans are pounding out great 'Mech design after great 'Mech design, often one's provided by Crucians. Hanse Davion calls for a Clan-Killer Heavy? Lyrans make it. Davion troops find plans for an incredible Assault 'Mech? Lyrans build it. There was pretty easily a lot of resentment to go around. Toss in a milktoast leader like Victor and it was pretty easy to see how Katherine could manipulate those feelings to her own advantage.