Play the last one enough and it gets really easy too. I one shot that every day with Full ship durability at the end. The only disappointing thing is that the last bonus to kill the 4 Tough fighters is bugged and doesn't count the 4th one
. Try to time your EMP in the very difficult mine field sections, make sure to use your recharge shield generator at smart times, and use the immune to damage thing when you really have to focus the last freighter thing.
Also, if you try to use Normal Missiles on Shield Generators in Clouds of Vorandu or whatever it's called, it automatically tries to assign proton torpedoes if you have them, and is incredibly annoying. I've been blowing up 3 plus the command deck before I even get past the gunner ships. Then I use normal missiles to kill the last generator. It takes a few fly-by's but it's doable.
It would be nice to have a few more missions available other than recycled ones, and to be able to acquire all the ship upgrades at lower lvls as well. Going from zero use abilities to all of them at 50 took some getting used to, especially because there were several missions that I could have used proton torpedoes on.
To the loot options, just buy the epic ship upgrades from the GTN. I could be wrong but I believe cybertech can make them all? The upgrade rewards you got were for first time completions of the missions, and the commendations you get reflect the base mission reward plus the bonuses you complete inside. They aren't random.