@Dietsoap I feel (of course, going on my knowledge of writing and plot conventions in texts, past and present, which partly I learned in University and partly I've experienced myself), is that Nagoshi had a fantastic plot and character introductions in the first game; with the many gameplay flaws of 1, the plot was just fantastic and still is.
Again no evidence, but I feel with 2, Nagoshi came up with characters and their motivations, then tasked Seishu (the crime writer brought in for the first game), to do MORE of the plot, characters and situations himself; can't remember where I read it, but he got more free reign on 2 than he did on 1.
The first half of the game is rock-solid, plot-wise; clear antagonists and situations, great setpieces and the characters are introduced quite well.
The second half, things fall apart; characters take a 180 in terms of behavior and motivations, the plot twists are all ridiculously over the top and BEYOND unbelievable (the series is full of ridiculous moments, but fake Kazuki gets shot in the head and doesn't die? WTF?). It says on Wikipedia they went for a more dramatic plot, but 3 is significantly more dramatic and it's done properly and realistically (hell, for the 90 millionth time lol, a similar situation was happening in Japan at that time as well, although no CIA involvement, of course).
For how stoic, intelligent, street smart and just overall genre-savvy Kiryu is as a character, when Kaoru gets hit by Takashima and he pulls a, "Kaoru!!" getting distracted and getting the gun (WHICH HE HAS STATED HE DOESN'T LIKE USING!!!!!!!! GRRRRR
) shot out of his hands, is just shoddy and not-nuanced writing and it still pisses me off.
That entire last chapter is deplorably-written and I felt that Seishu just didn't know what to write at that point... and when you don't know what to write, you just cobble a bunch of shit together, filled with shock and awe, which he did in spades.
But it didn't work; he was not asked back after that game and hasn't been involved since (thank God) and, IMO, the plots have been written and conceptualized brilliantly, (barring 4) from 3 and on.
TL;dr: Seishu screwed up on 2 because he didn't know what to write, so he threw in plot twists and made all the major players be completely opposite from how they were established to be.