I've just started this AP and have only completed session zero and 1. I'll also likely be transitioning toward the end of book 1 into homebrew campaign - not because Strength of Thousands doesn't look cool, but because I happen to have written my own campaign starting in Nantambu at the beginning of Covid, and had to cut it short on my first attempt at running it.
Anyway, I didn't change too much about the AP intro. I get what you mean that it's weird when one group of novice students keep running into weird and dangerous s#%!, but I find that can be helped by tying in character backstories in some ways. With the alterations I've made to the campaign, Teacher Ot is actually sort of responsible for the gremlins being around and messing with the cohort. He's still a nice guy, but is also tied in with doing some research on behalf of another, shadier organization in my campaign's big picture.
For the free cantrips, I agree that it feels a bit boring to just offer each character one of six cantrips as an innate ability, especially since 3 of my 4 players are spellcasters anyway, and are already a bit overwhelmed with the amount of stuff they can do.
What I did was:
A- increase the number of cantrips offered by Ot from 6 to 24. This is to make their choice feel more personal.
B- Add flavor. Ot pulls out a carved wooden cube with a symbol on each side. When a PC touches the symbol it lights up and unfolds into another set of four symbols. The one they choose will determine their cantrip. If they've already got that cantrip, it won't light up for them. Ot tells them that this magic flows directly from the Magaambya, but is theirs to share while they are at the campus. This ceremony also took place at the Circle with the crazy pillars, to connect it thematically with Jatembe's original magic.
C- Tell them that each of these cantrips is special. Aside from being an "innate" ability, I also intend for these cantrips to allow more flexibility, if not more raw power. Like, when a player would normally try to use a cantrip to do something not really covered by its rules, and you'd normally say "sorry, can't do it", in this case I'll allow an Arcana or Nature roll (or whatever skill is appropriate), and allow them to stretch or flex the result of the spell a bit on a good result. Once they've successfully flexed their cantrip in a particular way, it'll be easier for them to do that in the future.
The goal is to make them feel personally connected to this free cantrip, and to the school through it. In addition, I'm hoping they can show creativity with how they use their magic, which is a core principle of the Magaambya.