This is aimed more at AoR GMs than EoE or F&D, but feel free to pitch in...
Where do you set your game? Do you use a defined area such as sector, or roam galaxywide? I'm planning my next game and I'm thinking of focusing on a particular area, either a single sector or a group of sectors, and having the PCs be part of the Sector Force. My thinking is that they'll have an area they can become familiar with and can see real effects of what they're doing. Later on, as their contribution rank increases, they could be transferred to the control of Alliance High Command and operate on a galactic scale.