I realized I'd been doing something that wasn't clearly based in the rules...
When a bad guy (or minion group) gets taken out, I remove an initiative slot for their side.
If they have already acted in the turn when killed/stunned/ko'd/caused-to-flee, I pull the first slot for their side.
If they haven't acted, I pull the last slot.
This nicely contracts the slots.
Figured I'd share - and elicit comments.