In PotBS theres a couple missions that cause a permanent (yet restorable) change in your character. Like one where your leg gets amputated due to infection. I think That STO should get a few missions like this on down the line.
It's the 25th century, so the tech exists to restore your hand, leg, what have you. But during the mission you would have to deal with the issue of being disabled in a way. PotBS did this with having you do a couple missions to get your new wooden leg that looked just like a real leg. Imagine that, lol.
Maybe our captain could go through something similar to when Picard was tortured by cardassians. But not cardassians, because thats plagarism

This would also add material that we could include in our Bio's.
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Also, it would be great if there was a death of a BO or something at some point. I was flying around with the requisition new officers for 3 days, with 3 BO's just waiting to get picked up. I couldn't because my slots were full. BO death would cause these extras to be needed and mean more. I for one use the same 4 i used when i started.
BO's can be remade anyway.
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I always thought those missions in PotBS made the game really cool. It doesn't gimp your character, nor does it cause you adverse discomfort.