I can't help but think your not using everything you can...remember basic tactics.. manuver.. remember to rebalance your shields as ofen as possible..use sci team to regenerate shield, use power to shields, use everything.. I've beaten the mission at all rank levels on different toons. Whatever you do don't ever take the AI for granted.. it can out shoot you, and will use its special abilities..you have to out think it.. Most times take advantage of thefact the AI rarely repairs it ship.. and when it does so its by changing power presets. Take advantage of this and USE ALL your bridge officer special abilities.. if a SO of a bridge officer is not being used regularly then your ship is not going to be as effective in combat. If your not useing everything you can have your can have "those" days. Respec some bridge officers and train them back up.
If your science, you and your ship interfear with an apponents ability to damage through either effects aginst thier ability to fire, or spacial effects such as Tachy rift etc.
I strongly recommend a BO with the release warp plasma ability for facing a add the any AI
The stuff is hell on fighters and small ships. None to healthy for large ships either... More importantly is it stops them in space in most situations. Starships need to move and manuver to always be presenting a strong shield to the enemy..or a tremendous amount of firepower. Both if you can manage it.
A crusier class ship warrent eiother an engineer capation, or racials that provide extra power..warp theorist, tinkerer, the specific captain racial. Elusive is alwaysone of my favorites to take..Its a defensive buff.
When you have an ai immobilized you should manuver a line across one shield facing and pour on the firepower.
Shields strongly mitigate torpedo and mine damage.
Hold your torps for a down shield.
Drop mines if your overruning a target... if you dropped a shield going in the mines should hit for maximum damage.
If you hurt the ai with mines, it'll start shooting at mines. If its shooting at mines.. its not shooting at you!
If you have photonic fleet, use it.
if you have call reinforcement use it
If you have any terrain at all use it. A rock, a base..if you need to make time to repair us terran.. keep it between you and the enemy while you effectsome repairs. Shiftpower to shields and Aux to repair faster.
You can repair criticals in amission IF your not in combat (assuming your playing at the higher difficulty) just get beyond 10k range and stay there for a couple moments use your full speed button as your cue.
Once your "outof combat"" repair the crits and get back into the fight!
And here is a big big secret. Something some folks haven't quite figured out yet. If you have a programmable mouse, keyboard, etc.. don't use macro's.. Its a great way to get your bottom handed to you as the entree in PvP. And not a good idea really in PvE because it gets you into bad habits!
This is Trek, I'm sorry, but the presence of your brain is required. :

ointing a Klingon finger..Line delivered with a smile::
Hope that helped in some way. Mostly learn your sjhip, learn what it can do, what you can do. If it didn't work, there is ar reason. While your waiting for your ship to respawn you can think about how you could have done that better. And please.. please... EVERYBODY who has played has had several deaths in space combat.. It supposed to be hard!