I've been playing the PSP version of Uchikoshi's 12Riven ~ The Ψ Climinal of Integral, which is the last game he did before 999.
It really cements in my mind what a great writer he is. It's a sci-fi mystery (much less of a "thriller" than 999) and the plot has a few similarities to the Stephen King story "The Langoliers." But unlike Stephen King, Uchikoshi works out the physics of the game's sci-fi elements (to my satisfaction, at least) and explains them at great detail, which is really what I love about him. Unlike mainstream writers who are like "hey, the details of how the sci-fi elements work and the logistics of the villains' plans and whatnot... That's besides the point. It's about the characters and their journey." Uchikoshi exposes that for the bullshit copout that it is. I haven't finished it yet, so I don't know if there are gaping plot holes, but there have been lots of times where I've felt "this twist is ridiculous" and then two hours later: a full and satisfying explanation.
However, his tendency to overexplain everything can make for a really slow read. This is obviously typical of the genre, but I think Uchikoshi is particularly detail-oriented and 999 really benefited from both the faster pacing of having a story with an urgent time limit and having puzzle scenes that break up the conversation.
Having the dialogue be fully voiced is great, though. It really brings the characters to life.