Hmm, well that is a good point. An intelligent being may be able to figure out how to escape, in fact if you think about it, sapients would probably be taught how to escape the things in case they were captured! And likely at a very young age too. They could also have some sort of magic (like enchanted items) which protect them from being captured, or at the very least make it easier for them to escape.

And this all does bring about another interesting implication: people may actually allow themselves to be captured just to like sneak across borders or stuff like that. It could even be illegal to take crystals into prisons because they could be used to sneak people in or out, and also possibly illegal goods too assuming the things can also capture inanimate objects.

One thing I was thinking about before I even started this thread, though I really didn't like the idea, was that when a trainer summons a monster, he's not actually summoning the thing he defeated, he's summoning a copy of it. Essentially the monster he fights with is some kind of magical automaton that is a carbon copy of an actual living thing. But I didn't like the idea of the monsters being mindless constructs, and besides this opens up possibilities like them trying to find some way to create additional copies of 'captured' monsters.

The capturing soul thing actually makes the most sense. As has been mentioned, it would help explain why most trainers don't have more than 3 or 4 monsters, and the maximum possible seems to be six. This also kinda makes the whole capturing thing a bit more humane too. This could actually make the monster immortal, as long as the trainer lives. Also there is a possibility that if the trainer dies somehow (like he dies in a cave or somewhere else out in the wilds where no one will ever find his remains) the monsters could be freed immedietly, or go to the afterlife with him. I kinda like to think that's what the inhabitants of this conworld believe, though they don't actually have any way to verify it, its just a religious belief.

However, thinking about it, it does cause one obvious problem: how does he store monsters he's not carrying around with him? I guess you could say he can only have access to up to 6 at a time, no matter how large his actual collection may be, and needs to go to an alter or some-such to change them out.

I really do appreciate all the help by the way, you've all really done a lot to help me flesh this out.