I mulled this over for a couple of days and I really like the current aspect that right now it is a choice to drop off prisoners at closer colonies easily and have a higher risk of those going back to the race you captured the prisoners from if that colony is taken over. I think it would be awesome to play into that aspect more instead of or in addition to the interrogation aspect.
Can we make prisoners visible with sensors so mounting raids on colonies is more of a consideration? (I am presuming they are not visible currently as I cannot remember seeing any, but also cannot remember rescuing any from a colony)
I'm not sure if a rework on naval academies and crew is needed or not to help POWs become more important as there have been games where I run low and others where I run at highest base crew training and never run out. I do know that with it being easier to train up crew than previously and the cap being lowered it is definitely less of a bad thing when you have to lower crew grade or use conscripts for your ships.
Edit: Didn't realize a rules update had already been posted, but most of this still stands so I'll leave it here for consideration.