What you see in that picture is basically three design epochs, side by side. The first epoch is the Reconstruction epoch, the Deimos. The second epoch is the Post-Capella epoch, which includes the Atlantis and Barbados. The last epoch is the 'Shiny' epoch, which includes the Raynor, Hyperion, Chimera and that adorable little cruiser that Blowfish made.
By the time of Earth Defense we're just entering the Shiny epoch. There are very few Shiny ships; and hence very few uber blue beams. It really makes no sense equipping the entire fleet with the uber blue beams at this point.