Gorgon's hit on it, really. Some characters are 'known' to be important. Organisers, fixers, ideaologues etc. But there's often not much to hold them on, besides secondary evidence. The sort of thing which would not secure a conviction, but which constitutes reasonable suspicion. Building a case takes time and effort. You can't just tell them to stay put, because they'll disappear. And we're not talking about a bail jumper who might break a few windows. They might kill a few hundred people.
My point is really that if a case takes time and effort, but time can't reasonably be extended, then we need to increase our 'effort'. We need more officers and better liaisons. because apart from anything else even 90 days might not be enough in some cases.
But I need to think about this some more. I don't feel like my viewpoint is very deep.