Figuring out what scenes to have in the story depends mostly on two things:
- Knowing what you want to say
- Knowing how to say it
Creativity is of course also important, but there needs to be a mix of creativity and craftsmanship. In fact, I think it's about 10% creativity and 90% craft, or something like that.
What you want to say
What you want to say will tell you what interactions are interesting, what disasters and struggles to have in scenes. What people to follow, what places to write about. What subjects, problems, themes, and what lies and truths to embed in the story.
This part, I think, mostly comes down to who you are and what you want. For me, it's vital to have some kind of important message or political agenda. It's good for motivation, not so good if you're prone to soapboxing... I just personally feel, if I'm going to spend years working on a book, it'd better be something I really need to say...
I'm certain there are as many motivations and messages as there are writers out there, so go with what you have and make it stronger ;)
How to say it
When it comes to knowing how to say what you want to say, it's a bit easier. Here are some sources for scenes from the "craft of writing":
I use the Snowflake Method to get started with stuff like characters and plot points (as you've mentioned), as well as a storyline (one-sentence description of the whole work).
The snowflake is nice in that it asks for each major character's view of the story. This is great for looking at the story and the characters from different angles and usually shake loose things (scenes) I'd love to have and things I must have.
This is especially true if you treat each major character as the hero in their own story. Just beware of too many scenes, threads, POVs, and agendas. Try to keep it focused on the main character or at least on a theme (at least before you start writing, if you can't motivate having all threads you should cut, and that's easier before you've written a lot).
Story structure, as you've mentioned suggests several key scenes and plot points.
One of the more important plot points is the midpoint. So much happens here. The hero goes from reactive to proactive, if he chooses to follow a lie he's a tragic hero, and we can start suspecting how it all will end, even if we don't know all the details. We'll probably get all into the core and theme of the story in the choices made at the midpoint.
Check out James Scott Bells, "Write Your Novel From The Middle" and "The Moral Premise" by Stanley D Williams for input on the midpoint.
Another important source for scenes that should be in the story is the characters.
The plan of the antagonist is very important. My antagonists always have a plan! They're not just there to be irritants. They need something badly and they're not going to just step aside at the first sign of opposition.
I usually try to write the story so up to, and even past the midpoint the antagonist is the one behind the wheel and the protagonist only reacts to the effects of their plans. Only when the protagonist realizes the true nature of the conflict (in the midpoint) does she start to get more organized with her own plans and her opposition to the antagonist's plans.
It's good to have a strong antagonist, meaning that the protagonist will have to run from, evade, and avoid the actions of the antagonist, and likely cannot go straight at them at the first sign of antagonism.
The same goes for the protagonist's opposition. If the antagonist is strong, the protagonist will fail, several times before finally defeating the antagonist at the climactic moment.
You could always fill the second act with more disasters, setbacks, and problems for the protagonist and her helpers. And make sure the antagonist is the one to blame for it all!
Character arcs are also very important when it comes to what scenes should be in the story. If your character follows an arc (and at least one should—usually the main character) there are certain things your story should have.
For instance, you protagonist might want to reach a goal (based on her belief in a lie), but the truth she will believe in at the end of the story shows that there's something else, preferably diametrically opposite to, and utterly incompatible with what she wants that she needs in order to be able to follow that truth.
There also need to be temptations to draw the character back into the world of the lie, and she needs to prove that she does indeed believe in the truth in the end, preferably through some form of sacrifice (of the thing she wants that is blocking her access to the thing she needs).
You may also need to add scenes or add elements to existing scenes when you start finding the theme (which usually happens at the end of the first draft and may sometimes happen again in editing... and maybe even later than that...)
How many scenes the story should have
Finally, if you have a solid story now, but feel you have too few scenes, maybe this is a shorter story?
But sometimes it's hard to tell from the number of scenes how many words the book will have if the word count is an issue.
I don't know how many scenes you've come up with yet, but a scene might be longer than you think.
With my current WIP, I found myself thinking I was writing a shorter story, maybe too short, so I added scenes, an extra subplot, an interaction with the protagonist's mother, a trip...
I was hoping for 100k words. It ended up at 150k words... so my worries that it was too short was rather unfounded...