So far, Fate seems quite good as a starting point.
It would require quite a bit of alteration, but I can already see ways to change it so one player could be Kira (Individual), One could be L (Individual), one could be the Kira Investigation task force (Small Group), One could be the US Government (Large Group), ect.
We'd need a way to add rules for small and large groups, and of course, only the DM's and the player will see that players character sheet.
Wait, no, we just have a special version of minions for groups.
You know what, I'm just going to stop brainstorming until I've finished looking at the rules.
So far, a intrigue focused version of FATE seems damn perfect.