First, I'm fairly certain that I'm not the first to wish that one's starting Stress and Vitality Maximum could be 4 without having to spend a background point; in fact, I'd vote that reducing the starting value to 2 (and possibly dropping maximum Temperance and Endurance a point in the same blow) would be worth a bonus background point. As-is, it's annoying that I'm basically forced to spend a background point on every character build just to make sure that if I take a 2-3 point hit (say from Marchant bullying me) I don't get sick the next day automatically with no way to avoid it other than abusive levels of save-scumming. This was basically why I abandoned my first character attempt outright, I even missed my first day of school on that game!
Second, I'd love to see more flirtatious options in events and adventures. I just experienced Sententae, used Sleuth to confirm a girl had done the prank, and got horrifically disappointed that I couldn't say use a Flirt or Innuendo (to let her realize that I'm joking) roll to make a big joke out of "confessing my eternal love" (especially if netted me a bonus skill step in say Romance, Dating, Practical Jokes, or Playfulness along with improving my relationship with her) and dancing with her or something. I also remember having seen earlier an event where a girl's familiar stole my wand, and when I caught up with her I was given an option to try and blackmail her; even if it was limited to those with "on the prowl" (which admittedly I don't have on this character), there should've been an option to offer "I'll call it even for a kiss" with a Flirt roll that either gets a peck on the cheek before she runs off giggling or results in her running around embarrassing you by telling everyone how you're in love with her if you fail. Another such random event I saw involved a girl's hair being turned blue; it really seemed like a flirtatious option would've fit there perfectly, at least assuming one has that particular background component. In contrast, the event where a girl was upset that there was a false rumor of her having kissed someone did seem like it would've been awkward at best to insert something there, so no complaint on that one. I can understand wanting to minimize such activity with 11 year olds, which is why I wouldn't suggest more than words with giggles, blushes, and maybe one or two pecks on the cheek, but with the contrast of that other event I saw where Marchant was ambush-kissed by Joana and promptly fainted, it kind of feels like this area of characterization was abandoned after someone started to explore it, which is a real shame IMO.
Third, a few additional background ideas: 1, at least informing if not levels in all the Mastery skills would be nice; the best way I can think of without just creating a variant of the secret heritage background to do this would be to say your character got mixed up with a cult at some point (possibly also giving other skill boosts, such as Manipulation), albeit I can see why it might be difficult to figure out how to implement such a thing. 2, you were an outright bully at some point, with bonuses to Bully skills (at least Insult, Intimidation, and Tease) should exist (I'm thinking a Deed: Bully that also hits 2-3 random or bully-prone student relationships), and preferably change the part of the adventure with Oan so you have to pass some sort of Lie/Deceit/Acting/Bluff roll or her mouse bites you (for damage or no, I don't care), cutting off the adventure prematurely and possibly resulting in the quest chain derailing completely. 3, an Orphan option that disables Correspond and prevents you from also taking most if not any of the Family and Station options, but is balanced by big bonuses to thief-type skills so it doesn't actually have to grant a background bonus point; maybe the address on the letter then becomes where your family used to live before they died when you were a small child (and the new tenants were willing to let you use it like a PO box), maybe it's the orphanage you were taken to, after having lived on the streets for years, mere months before the letter arrivals.
Fourth, if the rumor I saw about there being special events during the summer are true, they should take all your background components and your actions at Academagia into account. If you're from a black sheep of a family of ill repute (Pirate Grave Robbers with Secret Heritage, for example) who is a known hero (Lone Sentinel, Negated, Prodigy: Spiritual, got the event where you reported to the captain of the guard on the Thieves Guild planning an assassination attempt), you should see the authorities come to your rescue; in contrast, if you're a black sheep of a family of good repute (Religious, any of the Descended options) and you have a bad rep (multiple demerits and reprimands, Life of Avarice, Secrets and Silence, maybe even Eclipse and/or Three Suns), it gets even worse for you.
I'll probably come back with more ideas later.
