Honestly that's this game and every game that it can claim inspiration from (The AI Somnium Files, Danganronpa, Ace Attorney, etc.). It's not really a weakness of the genre but more of a concession to make them accessible to the vast majority of players. The MO of any game like this is to create a mystery but not make it something that can't be figured out by a typical person with a some thought.

There's a market for super hard mystery games and they exist but it's very niche and wouldn't appeal to most of the people this game is aimed at. If they did that they'd be limiting their consumer base to a MUCH smaller group that could never make the money back on a game of this scale. It's about appealing to as many people as possible to be as profitable as possible.

If you want a super hard mystery those games do exist but probably not in this aesthetic and definitely not with this level of funding polish. Games that actually make you break out the pen and paper tend to be indie titles that have spartan UI's, rough visuals and everything else comes across as cheap. Because the person making it may have a great mind for mysteries but either lacks the skills or (again because of the niche market) the budget to wrap it up in the fancy exterior a more comprehensible title like this has.

That said to answer the original question; I'm about as far as you are and haven't found it particularly difficult. Honestly the Amaterasu Express, the tutorial essentially, had the potential to be deeper than the following two but because it was a tutorial the progression was very obvious. If it had been saved till later in the game when there were more things to deal with and the mystery was more obfuscated it could have been a decent little story. But with all that said I'm still enjoying it for what it is, I knew going in what I was getting into based on what inspired it. Sometimes something lighter instead of something super difficult and aggravating can be what the brain wants and needs, not everything has to be the Return of the Obra Dinn.