I'd like to second that upgrading of your space ship for missions. I tend to be time restricted on play so if i only have 10 minutes or so I'll try and rip one of quickly. I was struggling as well, and ship upgrades made the difference. The level 1's are all between 500 and 700 credits so it wasn't to onerous to get as many as I could. I completed one of the double missions and was rewarded with a blue ugrade. Saving up my fleet commendations for a proton torpedo launcher.
As some of the upgrades give you faster/more powerful blasters it pays off for taking down the fighters going after the shuttle. Extra missiles help in taking out the corvettes guns from a far as well.
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