This may be a dumb question, but does the difficulty level of the game increase at certain points along the way as you level? I ask because I just reached Commander 5 about an hour ago, and every mission since then has been incredibly tough. I had to take my Heavy Escort into the shop after a particularly tough fight and pull out my Heavy Cruiser. I just barely survived with that ship. I haven't had any problems with fights up until now.
I have felt it too, which I personally enjoy. The missions seem to progressively increase in difficulty as you level up. The way I look at it, you are getting more skills, harder hitting weapons, and more hardpoints on the ship to equip those weapons, so it should increase in difficulty. Even though there is no death penalty, I hate dying and do everything I can not to. I also keep it even more challenging by using only phaser type weapons on my ship to keep it in line with what the Federation would use.
The problem is that this has suddenly become ridiculous. I can't destroy a single +1 ship now, no matter what I do. I'm using my shields, positioning, debuffs, topedoes, Alpha, jam sensors, tractor beam, fire on my mark, everything, and I can't kill a Frigate, for crying out loud. What happened?
UPDATE: I went through all my ship components, and the only thing I had changed was dropping an Engineering Console (Tritanium Alloy Mk 3--5% dmg resistance to all energy) for a shield regeneration console. I replaced it, and I was fighting "back to normal". I had no idea a console could have that much of an effect on my ship!