Personally speaking, I like that the new challenges in story mode put my ship at risk. I
Me too, wish more of their changes (ever) were like that. Cryptic kinda sucks at understanding this. As you go into more difficult modes, the dream scenario would be for the AI to get smarter, or give the NPCs some flexibility so things aren't so predictable on every single STF run.
Instead, every single time they've tried to up the difficulty, what they'd gone with is just adding a ton more hitpoints to the bad guys, and giving them uber-guns so they can one-shot you even if you had 100% health beforehand. Only positive they've done is when they added timers and limits, and death penalties; that at least made things harder/more urgent. Giving each probe 1 million hit points and super torpedoes doesn't add challenge, just frustration.