As well as the idea from the wiki about having countdown's and
deadlines (resolve the conflict in 3 turns or something bad happens),
I've been having some success with another form of timer.

I use poker chips for keeping track of nemesis chi and mook threat
ratings. As they lose them, I remove the chips from the stack.

So I've started experimenting with having stacks with bands of colour.
For example: my CDC Death Squad mooks have ten Chi - four green on top
of six white - I tell the players I'll bring in the nemesis when all
the green are gone.

It means that if the players are doing appallingly with dice rolls,
they get a bit of breathing space before the big bad. But if they are
on a roll, they can bring in the nemesis early, and get a head start.