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I'm trying to add good amount of choices to my new story, and I would appreciate advice on how to make choices with significance so the reader could actually direct the story.

There's a very simple answer to this: choices matter if they change the story. That's it. As for the types of choices you could implement, there are a number of them ranging from insignificant to extremely significant:

1. False choices
This is where your choice isn't really a choice. You present the reader with two options, but no matter what they click, the next page is the exact same. Example: The protagonist speaks to another character about something and they get to choose between insulting or complimenting them. Yet, on the next page, no matter what choice was made, it is revealed the other character is deaf and couldn't hear them anyway. The story progresses as if the choice didn't exist.

2. Cosmetic choices
These are choices that change surface-level text but doesn't impact the overall substance of the story. For instance, this might be choosing the character's name and having it mentioned later in the story. The actual content and plot doesn't change because of this choice, so it has very little significance on the story.

3. Info-link choices
In stories with unique worldbuilding or a character investigating a situation, there may be choices purely to find out more information about the world/ situation they are in. Once again, this wouldn't impact the actual story itself, although it enhances the reader's experience of it by providing more background information on the topic. Usually, these choices would have a 'previous page' link at the end of it, returning the reader to the story with slightly more knowledge about the fictional world. 

4. Bottlenecks
You can find out more about the different types of storygame structures by clicking this link (it came from this article which I also recommend reading). Essentially, bottleneck choices are those that seem to lead to unique page(s)/ scene(s), however, they end up looping back into the main narrative. This does change the plot and perhaps character development to some extent---depending on what happens in the scenes before the reader is led back to the original story---yet the ending often remains unchanged (unless it is paired with a cosmetic choice where this previous choice is referenced, making it also fall into the category of #7). 

5. Dead ends/ death scenes
This one is pretty self-explanatory. If the reader makes a wrong choice, it could result in a premature ending or the death of the protagonist. It could be as simple as 'a stone crushed you and you died' or as complex as a whole series of events leading to the protagonist's decision to abandon their main storyline and settle for a mediocre existence. But when doing this, beware of making it too random. Readers would hate for a seemingly meaningless 'left vs right' choice to be the difference between death and life. This honestly goes for all your choices. If you want to make them meaningful, you have to foreshadow the consequences properly through the narrative; give readers some context for the choices they're choosing between.

6. Delayed consequences
Sometimes, a decision that readers make would not have an immediate impact, but changes the trajectory of the story in the future. Let's revisit the earlier example of the conversation with a deaf character. It might turn out that later in the story, there is a plot twist where the character was a spy who was only pretending to be deaf all along. Then depending on your earlier action, they might kill you or let you live. That's a basic example of delayed consequences. It might also be worth making a previous choice affect several different plot points. This can be found in stats-based stories (like Price of Freedom, which you read), where choosing between options would give you a number of points for each stat. Then, this number affects the options you get later on in the narrative.

7. True branches
These are the choices that have the most significant impact. They completely change the trajectory of the story, branching out into a new direction. In a way, I tend to view them as mini-stories or parallel universes. An example is a character choosing between playing a detective or a murderer. Then the reader has a completely different experience based on what they chose: the detective's story is focused on solving the mystery, whereas the murderer's revolves around attempting to get away with their crime. Most of the stories on the site with a cave-of-time structure tend to use true branches.

As for more general feedback on making choices matter, ensure the stakes are high enough for the story. This doesn't mean everything has to be a life or death situation, but the choices do have to impact the character's goals, bringing them closer or further away from achieving them. A story where the character only gets to choose things like what to wear or what to eat wouldn't make the reader feel like they have much control over the story (though exceptions could exist, of course). 

If you want to take it a step further, tie your choices into the theme and character development of the story. If your protagonist's internal conflict is between their tendency to distrust everyone vs the desire for connection, then you could make your choices reflect this. Let them have moments where they choose between telling their secret to another character or withholding it. Or perhaps if your theme is about the importance of thinking for oneself, your character might start off being naive and easily mislead, hence the starting choices would be made out of naivety. Yet as the story progresses, they can choose to make more choices that go against the group mentality, and eventually, readers will be presented with a choice at the end which completely juxtaposes the choices at the start.

Hopefully this answers your question. Tbh I just wanted to write down about the different types of choices I've seen, as a way to remind myself of what I could incorporate in future stories. As for the site regulars, do let me know if I've missed any other types of choices. 

Wow thank you sooo much for this breakdown, Mystic.  

This is a great breakdown, Mystic saved me the bother of an effortpost. Here's some additional thoughts:

For my part I consider only types 5, 6, and 7 to be meaningful choices, and type 5 is frankly on thin ice, since it just leads to a dead end. So if you want to create a story that has a lot of choices, and for all those choices to be meaningful, here's some options:

1) Have a lot of type 5 choices, and some type 7 choices at key points. This one of the most favored models on this site, since it has a low burden on the author, and allows the reader to manageably explore every branch while still having plenty of agency. The downside is that, as I said above, some people don't consider type 5 choices to be meaningful.

2) Use variables to make the majority of your choices type 6 choices. This is a little more work since it requires you learn how to use the advanced editor, but it's a really good way to make sure every choice is important. You'll probably also want to sprinkle in some type 5 and type 7 choices for variety, but you can make those influenced by variables too.

Here are some ways you can use variables to make a lot of type 6 choices:

   A) Player stats. Have choices impact stats, and make future choices & success rates influenced by those stats. For example, choosing to train increases your strength stat, which then unlocks the future option to bend steel bars; or makes it more likely that you will succeed at doing so. Alternatively, making a poor choice might penalize your stats.

   B) Relationship trackers. This is the same as option A, but instead, the variables track your relationship with major side characters. Things you say and do will positively or negatively impact what they think of you. If you have a high value they'll be more helpful, and you'll unlock extra options with them. If it's low, they might refuse to help you, or betray you at a key juncture.

   C) Ending trackers. These variables are similar, but don't become important until the end. Say you have one ending where the protagonist becomes a professional baker. You might increase the baker ending variable every time they choose to make cookies or buy a spatula. Then if at the end the baker variable is above a certain threshold, the baker ending is unlocked. You can combine this with stats and relationship trackers too.

   D) Items. Again, this requires some scripting knowledge, but what items a player does and doesn't find can go a long way towards increasing player agency.

In sum: choices affect hidden variables. Then, those hidden variables influence later outcomes, such as by unlocking or restricting certain options, making chances of success for a certain choice higher or lower, or unlocking certain endings.

3) Time limits. Give the player a limited amount of clicks to accomplish their goals. Then, every choice matters because there is a limited clock. Will11's detective series does this.

The best way to make your game feel interactive is to give the audience the chance to meaningfully develop the protagonist in different and mutually exclusive ways. A story, basically, is the process by which a character becomes a different person. This has been almost all stories, since we started telling them. The Epic of Gilgamesh is one of the first written documents available to us (relatively speaking) -- it's about a gigachad demigod who learns to stop stealing people's wives and accept his own mortality. A story requires change in its protagonist otherwise it sucks fucking ass.  

In the medium of interactive fiction, the audience gets to choose what path the character takes, obviously. What that really means is they get to pick between two stories. From Paragraph 1, we have learned that a story is really just a journey a character goes on that changes them in some way. So a meaningful choice should offer the player the ability to set the protagonist off on completely different directions; they should be doing different stuff, and becoming a different kind of person. These options must be different from each other, so as not to bore the audience with recycled content, and they need to be mutually exclusive. That means that the possibilities offered by one choice must be closed off forever to the protagonist - that's what gives the choice weight and meaning. You should read Eternal by EndMaster for a really textbook and excellent execution of what I'm talking about here; the protagonist of Eternal is a radically different kind of character at the end of every ending.