A perspective that applies better to games focused on story than to games focused on puzzles:
If you're skillful in constructing your narrative, the pacing will fall out of the structure of that narrative—because pacing and structure are more or less the same thing. Think about movies and TV shows: You can flip to a channel and guess, after watching maybe only a few seconds, whether you're seeing the beginning of a story or the end. You know right away that you're in the back half of an episode of Law & Order because the action is in a courtroom instead of a smoky holding cell, but you can even tell how far into the back half you are, based on how angry Sam Waterston is.
Or think about Counterfeit Monkey. I actually don't remember whether Counterfeit Monkey used points, but I do remember how the story moved from a period of exposition, to a period of rising action, to a climax, and finally to a resolution and epilogue. You always know where in the story you are, because of the tone of the narration, the security or desperation of your situation, and even the mechanics.
Counterfeit Mokey spoilers in rot-13: Cnpvat pbzrf npebff va gur zrpunavpf guebhtu gur vapernfvatyl cbjreshy chmmyr-fbyivat novyvgvrf tenagrq gb lbh. N yrggre-erzbire vf phgr, ohg yvzvgrq va fpbcr; gur flabalz-znyyrg vf na rkpvgvat hctenqr, ohg lbh nera'g nyybjrq gb pneel vg nebhaq jvgu lbh. Ohg gura lbh trg lbhe unaqf ba gur nantenz tha, naq vg znxrf lbh srry yvxr Wbua Enzob!—naq lbh nyfb xabj lbh'er arne gur raq bs gur tnzr.
If you start out writing with a clear vision of your story's structure, that structure will inform the choices you make all the way down the line, and the players will be able to see it too.