The rule of thumb I use for short stories is that every single sentence should either add to your theme, build your setting, or give insight into your character, while progressing the plot. Let me try and explain by working through your example.
Note that everyone writes differently, and this is only my opinion - hopefully the comments elucidate my point and are helpful to others, instead of simply being "do this" or "do that" kind of feedback.
Eri glanced at her watch. Half past four. She'd been in the subway since morning, doing nothing in particular—just watching trains come and go, people getting on and off. A typical commuting scene. Though Eri had always seen the subway in a different way. To her, it was the place where the flow of time temporarily stopped. The platform where life paused as one selected the next destination.
On the whole (I'm not going to pick at grammar or oddly phrased sentences here) this is a good paragraph to set the scene and theme. We know the theme will be based around the flow of time in some way. Each action and description reflects that, so there's no need to cut anything.
Perhaps that was the reason she had stayed here for so long; she secretly wished time to come to an halt. But why did she want that? What she was afraid of?
This is rather unsubtle. You're telling, not showing. It's better to show us her hesitation, her unwillingness to step on a train lest time start moving again. That kills two birds with one stone - you get your "the train arrived and Eri got on" action, but this time it has import. Her action has meaning within the greater context of things. Those are the kind of actions and descriptions you want.
The train arrived shortly after, and Eri got on it. As they exit the station, she looked outside, but all she could see was a fast moving blur. Cars, buildings, trees, they no longer formed a coherent image. Or at least not one she could recognize.
As I mentioned above, each action you describe should contribute to the greater context. The description about the scenery passing in a blur contrasts wonderfully with the start where you talk about how in the station, it seems as though time's stopped. Hence, you'd keep them.
Once reaching Akigawa Station, Eri headed to exit number three and waited there. She glanced at her watch. She had arrived a few minutes earlier. Short of things to do, she watched people pass by.
These actions are necessary to progress the plot, but you use a lot of simple sentences which don't add to the setting or theme. You were talking about the flow of time earlier - tie it in! (Obviously, if your main theme is something else, then adapt as necessary.)
She's arrived early, so can you use that? Or perhaps you can describe the brisk pace of the people around her and how it makes her feel like she's being swept along in time's inevitable flow. You get the idea.
Or you could use it to build your setting instead. Do you want to highlight the decay of the city? Describe the tunnel(s) or building she walks through to get to the exit accordingly. Rusted pipes, scraps of garbage, etc. Or maybe you want to highlight the false face the city shows. Then you'd talk about the flashing ads, clean white decor and shiny floors, and contrast with bits and pieces that seem out of place for such a place.
She thought about the earthquake again. She thought about how each one of them had experienced something she hadn't. A crucial event in the collective memory of the city. Would she ever be able to interact with them the same way as before?
How does this tie in with your theme? At first I thought the story was about time, but now it seems like we're moving into memories and inter-personal relationships. If this reflection doesn't play a crucial part in the story, time to cut your darlings. If it does, then you need a much stronger link between your initial talk of time's flow and these thoughts. Thematic consistency good. Jumping randomly from theme to theme bad.
Before long, a gray Toyota stopped along the sidewalk. It was Eri's father. She rushed down the steps, and leaped inside the car.
Again, actions without import. If you're going to introduce her father, and the car, give them both meaning. Perhaps the car swerves out from the stream of others on the main road to pull alongside her. (Stream of time, yeah? Though you can probably think of a better action.) Or if you did bring the story across into the memories/relationships territory, then you can draw on the impending meeting between Eri and her father as context for these actions.
Hope that helps explain it somewhat!