It's not about having a strong fleet puts you at a disadvantage, it's having more than two strong fleets puts you at a disadvantage.
If you have two maxed out fleets, then you can potentially beat there's and not lose yours giving you a huge swing.
If you have all the sith, all the bounty hunters, all the rebel and all the republic ships maxed out then I grant you, that a big wack of your gp you won't be using.
But the only GA round i've lost, I lost on fleets not the ground.