Rewatched Crossfire, Prime says they dont have the resources to keep their enemies prisoners. What about the immobilizer? It worked pretty fine in getting them back to normal, pretty sure it would work just as fine in immobilizing prisoners. And I doubt they would have problems with storage either or maintenance, since the base is pretty spacious and since the prisoner would be in a form of stasis then their energon consumption would be very minimal.

 

I suspect it's a moral issue; was it mentioned if those under its effect are aware of what's going on? Because if so, Optimus probably doesn't like the idea of trapping an enemie's mind within a frozen body for however long they have them for.

Sure, it'd be useful to keep foes prisoner, but the Autobots may not like the concept of putting a Decepticin under a I MUST SCREAM scenario.

That's all I got, really. Maybe they just forgot about it  

 

The smart thing to do would be to get some more of those Insecticon pods and use them to put prisoners in stasis.

 

Well, they'd probably just waste away and eventually die. I mean, if you were stand still for months on end, you're probably going to starve, be malnourished, and more than likely a couple other side effects. I don't think Prime would get behind it at all.

 

Apparently just killing them is out of the question even though they've killed hundreds and hundreds of Vehicons.

For keeping prisoners it might be a space issue but IDK how big the base is.