The prologue will not change as the fact you are a stranger who just entered into their world through a portal left open by Zorro and them having no clue who you are or what you'll do or tell people. Their lack of trust of you lends way to a tutorial that shows you how things work while also letting you make mistakes during it to show if you mess things up, the story will continue on.
It also states they have no real exception of you and are just using you whether you come out on top or fail. The first task is just merely telling you to explore and do other things before doing the main quest without telling you. Then the second is have you done that and puts it in a more obvious way, more than just getting the puzzle right. The only point of those was just to explain go do others.
However, the fact others are willing to help knowing your plight while not putting themselves in danger for someone who they barely know for no good reason considering the line of work they do. The fact they keep pointing out you're not the first person to find themselves in this position is supposed to tell it's sort of a common thing that happens, and they've become less sympathetic, aside from Duilio, to your issue other than doing the bits to help you while they continue to do things they want to.
For Gen's case, while he knows your situation, your not the first. He had to change his plans ever since you got here and isn't the most happiest of guys having to do so. Having to constantly having to change his plans to accommodate the next new guy who wandered into Zorro's portal isn't something he wants to do, so dusts anything he can off to others, while just giving you the need to know information.
I could have just outright said all the context hints going on, and with the amount of people not catching onto them probably would have been the more obvious answer. Idk, maybe I'll put it somewhere else of someone telling you what you should have picked up and see how people react.
The previous plot was you wander around and stuff happens as it was made based off of Aqua Team Huger Force's original plot, but that upset a lot more people. So for people who already know about the group being not the most legal of people, and doing things that would otherwise land them in jail, them treating you as they do is a more realistic option especially when later on when you learn of this and more people start to tell you this like they used to.
Ultimately having you stuck in their group somehow because you worked with them and knowledge you know preventing any ignorance is bliss.
I could have conveyed this better with putting characters who naturally would just tell you more outright, instead of the ones who tell you by action, at the start. But I never really liked how people just tell you everything in games while knowing nothing of you.
The spelling and grammar errors will change.