Thanks for the feedback!
Per your guys' suggestions, flack burst has been massively buffed. Level 1 now insta-kills raider (I believe that before a full health one would survive) It also had its range increased. Because there are so many raiders, and they rebuild so fast, it hopefully won't totally negate the raiders, but it should make them much more managable.
The nukes now have longer range, but a much longer cool-down and a much higher anti-matter cost.
All capital ships are getting huge buffs in health, armor, and the number of targets they can fire at at once. For instance, the Galactica now starts with 25k health and 20 armor, with all other Colonial caps somewhere below that. The Cylons start at 19k health and 18 armor for the Basestar, if I remember correctly. All capital ships are now more expensive.
Colonial fighters+bombers also got buffed. They have a lot more health (almost that of a small frigate) and there are a couple more of them in a squadron, so you hopefully won't be losing all of them to the masses of raiders.
I plan on having another update out within a couple of days, to get feedback on these changes.