Woo, nice, you kept writing. Will see what I can add. Post Writing Note - I nitpick more this time around, tell me if it is useful or just annoying. xD
Start
The start definitely looks better now. Helps establish things in a more show than tell way. There being more nods at the futuristic setting is also nice. Credits also helps point at a future setting, and is way less jarring than Dome money.
Academy
Bored adult on train gets very little description, so without you explicitly stating later if I am meeting them again, I won't know. Obviously, they might not be important in anyway, just a normal supervisor of the academy or whatever. However, if they are an important character and you wanted to give us a sneak peak, you might want to just give an extra sentence to help give him more of a character to them than just 'bored'.
I will also mention that I wonder how someone ends up with the name Merlin in a future setting. I mean, it is fine, name your characters what you want, and honestly getting good names can be a challenge. It is just that I personally find it weird, since the presidents parents basically named their kid after a character that they really liked. Wonder if the doctor/nurse found it strange when they saw their name application (or whatever is handed over when a baby is born).
Description/Pacing
I feel I should mention that I like the way you are handling descriptions so far. It isn't drawn out but there is still enough to form a picture in my head. I do think my view on this is heavily influenced by it being used at the start of the story, as at this point in time you generally want to have things progressing at a decent rate, to keep readers interested as they learn more so that they can get invested.
However, I do worry that if the descriptions stay at this level the whole time it might lead to the story feeling bland later on, when I end up being more invested and wanting more heavy details. With that said, who knows, I might be worrying for no good reason. Since you have mentioned having a plot in mind, it should turn out well as long as you can execute that well.
Gameplay
So far it mainly seems to be a "here is a page with many choices, pick as many as you want" type thing. Nothing wrong with that, I just do wonder how much of an impact these choices will actually have. You are obviously using variables (probably scripting too?) which makes me worried, as there are many bad ways for this to turn out (and many good ways of course, but I like to worry), such as: a highly linear story, a convoluted story with useless variables, or an extremely branching story that will end up never getting finished. Just don't forget about the bigger picture and you should be fine.
Also, it does look like a bottle neck style CYOA, which I like, so honestly, as long as you spend some time thinking about why you are offering choices and what you plan to do with them it should turn out well. I will mention having choices to grant the illusion of choice isn't necessarily bad either. Oh also, I like that my character stealing was mentioned on the train (using on page variables text thing, I assume,) which is nice. I also stole the wallet this read again as I assumed it wouldn't matter, but would just give me more money, yet that text addition made me think that it could end up mattering after all! Even if it doesn't, still a nice mention.
The Opposition
Is this what the 'bad guys' will be called? Just sounds... odd. Like, is their organisation/group/party called "the Opposition"? Since such a name for a group just wouldn't make sense if they end up truly wining, since then they won't have opposition which means they aren't 'the opposition' to anyone. I don't know, might be overthinking it. Heck, if there is a reason for that name it might even be a good name, but so far it just jolts me a little when I read it. Also, it read fine in the newspaper, but I wasn't reading it as their name then, but rather a description of what they were, in regards to the academy.
Shop
Oh also, asking for 100 credits from twelve year old's to tell them political propaganda seems really weird to me. Like, how did such a deal come about? Did the Opposition walk up to a random shopkeeper in the academy and go:
"Hey you, here, see this piece of paper? Read it aloud to new students in order to implant ideas into their heads. I'll make it worth your while."
"Oh sure, but I'll charge them for it so I make even more money!"
"..."
"What?"
"Genius! Just remember, you don't know me." *end scene*
Great, now I am wondering about the world's economy. Is 1 credit == 1$? Or is it different? Since 100 bucks for a few sentences that seem to be something the source would want given away for free seems odd. I might have misunderstood something, or be thinking about this the wrong way. Also I do wonder if me paying for that information is tracked by a variable, hmm. Anyway... moving on. (Oh also, the credit economy doesn't really matter, it is not the focus of the story, just make sure stuff costs makes sense relative to the costs of other things).
Schedule
I wonder what font you used for this. Granted, it is a schedule given to kids, so it isn't immersion breaking or anything. I just wonder if it is a font that an organisation would use on a schedule for kids irl. This is a bit of a nitpick, but the main thing is for you to consider if it makes sense to you. If you see nothing wrong with it don't change it, I'm no expert but am just questioning it for the sake of questioning it.
While I'm here, I might as well mention... how long are the periods? Like obviously no one expects you to make the perfect education system schedule or anything, but I'm just curious if "common education" is given the same time allocation as "superhero theory" or "breakfast". OK, I do assume that eating takes less time than learning, but lack of time allocation on a schedule is interesting.
Heck, while I am nitpicking I might mention that it is odd that they don't let you upload this stuff on your PIP (good acronym btw). It is the future with handed out schedules which don't tell you when but only where! Anyway, I will say that coming up with time allocation would be pretty tough, as you do need to make it up and leaving it open can be very helpful in regards to writing the scenes. Vagueness is a powerful tool that you can use of in writing way more than in some other media (like movies, where timing is huge). Honestly tho, you probably don't need to worry about this at the moment. Just think about it if you want.
School
Wish my school gave me money when I done well on assignments... obviously this is a good game mechanic, since it lets you give readers credits, but thinking of it from a world perspective, I wonder why you had to pay for the form if they'll give you many times that amount latter (I am assuming at the moment that they will, at least). Also, the government must be loaded to be able to pay people for education regarding superpowers, tho to be fair it is probably covered by the military budget (cough*socialcommentaryignoreme*cough). However, keeping this system in might actually be a good idea, as again, it makes sense game wise, need a way to earn credits after all (and it does help to not have some other crazy way to earn creds instead).
PLOT
Oh also, I'm gonna say some guesses regarding where this is going, so you can see if I made correct assumptions or not as a reader. So... spoilers ahead... maybe.
The Opposition is actually the good guys, Lydia is the daughter of someone important (and is part of the Opposition), my family will not be mentioned ever again except maybe in some hostage situation, Merlin is secretly either really good or really evil. Hmm, what else can I come up with... ugh, there will be two main paths, one where I work for the Academy, the other where I work for the Opposition, unless you are partially crazy and offer a THIRD main path where I make my own faction or something. Anyway, those are my main thoughts.
Oh quick addition, I thought of Lydia as crazy when she said it was all lies, so I went back to the shop (go back button) to buy the information to see if I would think differently if I had heard that, I didn't. Obviously there is a limit to how much tracking you can do regarding stuff, since you want to avoid swamping yourself, but I am mentioning this since it stood out a bit to me.
Items
Adding this before posting, just wanted to say that items appear pretty useless at the moment, but if I am honest I barely tried to use them. I did try giving the book to Lydia when she mentioned using up all her money that she was saving for a book, but I didn't think it'd work due to the last sentence on that page, but I still tried. Hmm... now I think Lydia isn't important as she can't afford a book (tho plenty of ways to explain this away, so won't edit past part).
Conclusion
Definitely on the right path, your reply in this thread and seeing what you have added has increased my hope that this will actually be good. My expectations are now rising, hope they don't end up shattering from a fall. As such, keep writing! Finally, as I will never stop mentioning, remember to proofread at the end (and throughout). With all that, good luck and keep writing!
TL;DR
It has gotten better, I am more confident this will turn out well now as well. So keep writing and proofread at the end to ensure it all connects well.
P.S. Adding more to the descriptions/pacing part, I tend to go overboard in the wrong places when writing descriptions myself, so my worries might be just me comparing your writing to mine, and thinking that you might end up going down the wrong path since it isn't what I do. Can you see the issue with this? Anyway, main thing, remember to proofread at the end to see how it all ends up fitting together. That way you can fix any pacing issues that may arise, by altering the way you give descriptions as necessary.
P.P.S. Hmm... if bitcoin/cryptocurrency becomes huge it will be very weird for people in the future to read this story, they'll wonder what sort of idiot still has a wallet with 150 bucks in it. I am sorta joking here btw, obviously times change and people in the future should be smart enough to notice the publish date, but I just felt like mentioning this after writing the economy part under shop.
P.P.P.S. Hope you get something useful out of this, feels like I might have rambled a bit, but I still stand by my points until they are shot down. Anyway, that is all! Good luck writing.