really? weird. I distinctly remember researching live aliens again and again and again... and I think I never encountered a situation where the containment was "full", I always wondered how they fit those 20+ aliens in there. I know apocalypse handled that differently, but I can't remember how exactly.
the question is, how do we want to do it? do we want limited space in the containment?
if yes, we definitely need some kind of alien containment inventory management, including killing "unwanted aliens" (boy, does that sound terrible only to my german-we-have-a-really-bad-history-and-think-too-much-about-it-sometimes ears or is it the same with you?) when you bring home a high-ranking alien and don't really have space for it.
I'd also love to see the captured aliens in a base defense mission! maybe the attackers could even free them somehow, so if you're in a base defense mission and things are going so-so you would sometimes have to consider throwing a high explosive into the containment facility to prevent the live captured aliens from escaping and overwhelming you.