Let's start with the argument with Ema at the crime scene. The way to proceed is to present the Barricaded Door to tell her that the victim couldn't have possibly barricaded the door from the outside and ended up inside, which proves it was murder. This is contradiction is perfectly logical and good per se, but the piece of evidence in the Court Record could really use some refining. I assumed the planks and boards were inside the room, not outside, so it never occurred to me that it couldn't have been suicide. After all, it was suggested to be a locked room mystery, where the door is locked from the inside.
The trial begins, and Ema tells us that the victim presented several symptoms of depression: lack of appetite and some more things I don't remember right now. The autopsy report that we get when she's finished talking notes that the victim presented symptoms of depression, and that's good because it is used later in the trial to disprove the otaku's testimony... except the report doesn't specify "lack of appetite", it just says the victim suffered from depression, in general. This forces the player to remember a non-highlighted remark of many from much earlier in the trial, and by the time the otaku says the victim entered a restaurant, the player has most likely forgot that detail because all that's been going on.
Naota comes to the stand, and he gives a pretty long testimony. This goes beyond challenging: it is daunting and exhausting, made worse by the impending penalties you might get for pressing harder and the abundance of penalizing evidence-presenting traps. Not to mention that the testimony can be lengthened even more, so the player ends up with a thousand and one details to keep up with. This makes it extremely easy to forget or miss the "I knew about this suicide note I shouldn't know about" slip of the tongue, and I personally had to proceed by trial and error... which made me forget about almost all details our hooded friend told us.
When Naota testifies about hiding inside a closet while the murder was happening, I could see the problem immediately: he states that the defendant made it look like a suicide, yet he didn't dispose of the dying message pointing at him. I presented it, but I got a penalty. I saw no other contradiction, so I had to trial and error this one too. And I was very disappointed to see that I was correct, but the game expected me to present the dying message in a completely unrelated statement: the one where he says he snuck out of the room while the defendant was busy doing who-knows-what. Big mistake.
The next complaints are not objectively bad, I suppose, but are pet peeves of mine.
First, the player should never be penalized for wanting to get more information (pressing) - that undermines the point of playing detective, having all clues. This is something that even the official games do bad, in my opinion, so it's not limited to fan cases at all. I wish this mechanic didn't exist in either medium.
Second, the counter cross-examination, while a nice concept, penalizes the player for not guessing that an ensuing conversation will derail into irrelevance. I personally didn't see any reliable way to tell when something was going to be relevant or not, and I preferred not objecting for the sake of objecting, so this felt unfair to me.
Third, the trolling subversion of Ace Attorney standards. By this I mean, at the end of the trial, the player is asked to explain a contradiction by saying that the meeting is wrong, the recording is wrong, or that both are correct. As far as I remember, every single time Ace Attorney games give you this option, "both are correct" is the correct answer, but I got a game over by trusting the classics. This in itself isn't that bad because I just had to reload a save, but I was so annoyed by the previous mistakes that I took this one worse than usual. And this isn't the only example: before this part, you're asked to say if there is a problem with the recording or not. Again, as far as I remember, the official games always make you choose "I have no problem/evidence" in seemingly desperate situations. And again, I know this might have been a harmless one-off trolling, but I was already pissed off about the previous mistakes of the logic and this didn't help fix things at all.
Finally, the black box mystery near the end. I admit it's a cool idea to make the player think about how a seemingly perfect recording can be flawed, but the sheer amount of options to choose from in this part and the vagueness of what you are asked to present made this impossible to solve. I had to resort to the walkthrough for the first time, because I would never have presented profiles at this point. I think the official games would have pulled this off with much more user-friendly prompts and hints to guide the player through the process, instead of making them figure everything out at once. It also doesn't help that I thought that the recording information in the Court Record was just an excerpt from the whole 3-day footage - I didn't think the victim coming into his house way before midnight would have been mentioned in court if it happened.