Pretty fun game so far, I like the attention and level of detail in the prologue.
I think some people are getting the wrong idea about the choices we get during the prologue, I feel like we're only meant to interact with things in a superficial level at this point, the main story hasn't even properly started yet. Getting every choice you make to have permanent and significant repercussions is not workable with the level of detail this game is aiming for in my opinion, so I think it is fine for some decisions to only lead to slightly different dialogue or other minor effects.
I'd be okay if the full effect of reading Varion's scroll 2 is just that after the time skip Tali is also a bit colder towards Varion and not wondering so much about why they are not close anymore.
I also like the idea that the reward for suspecting Alva is loyal to Varion and not to Tali could be as simple as not gifting her the better sword, presumably if we keep the better sword then we can equip Felix with it in the future.
The choice of which lesson to take seems a bit more important though so I agree it would be neat if each lesson could result in different rewards, here are some ideas:
Studying scriptures - Allows Tali to impress the high priestess, perhaps she can gift Tali with an equipment of some sort.
Combat training - I'm not sure if the fight against the assassins has been removed or not (I didn't run into it), would be cool if combat training allowed Tali to take out 1 or 2 of them on her own with a prepared spell and potentially drop some kind of reward from them.
History - I can't really think of a very imediate reward for it, I think it would be cool if Tali being aware of the trial meant that she could publically expose just how flimsy the justification for Varion's coup is when he challenges her during the coronation, that could set some kind of [Tali sympathizers] flag which could cause some NPCs throughout the story to give Tali their support (with items and other rewards), as more people see Varion's rule as illegitimate.
Finally, I think the only criticism I have right now regarding the tone of the game, is that I feel there is a bit of a dissonance between the level of attention to detail the game requires from the player, and how little intelligence Tali shows as the protagonist of the game. I wouldn't mind if Tali was allowed to appear insightful a bit more often, could get annoying if the game keeps encouraging the player to be smart and pay attention, but then the MC keeps acting flabbergasted about revelations the player already figured out 20 minutes ago and having to have everything be pointed out and explained to her by another character. Maybe a more insightful Tali won't fit the main party dynamics that you have planned for this game (since in RtD Tali was pretty much the "flustered submissive" of the group), but I think it is worth keeping it in mind before making her too much of a "ditz" in her dialogue and interactions.