Choice of Ninja was the 13th or so Choicescript game put out, and I found it one of the weakest games at first, but it grew on me as I played.
I happened to play this as I was watching Naruto Shippuden for the first time, and the parallels are easily visible. You play a young orphan raised in a village in the woods, and it starts with you having to pass a test at your school to become a full ninja. There is magic, most of which involves invisibility, but becoming a duplicate is another skill. There are other parallels, like escorting a crotchety old man and dealing with a friend on the dark side.
But in a lot of ways its more realistic. Evil monsters are hinted at but not shown. There's no real magic past stealth magic and duplicate magic. So the over-the-top magical fantasy of stories like Naruto are toned down, and the parallels become less and less as you play.
The last half of the game is where I feel like it came into its own. Other reviewers have said that this game is very linear, and choices don't matter, but I felt like my choices mattered quite a bit when it came to the plans on infiltrating the final fortress. It was fun.
That said, I don't think this one holds up as well as other older Choicescript games, especially when compared to Slammed!, which came out around the same time. Slammed! is in the top 5% of all IF games ever, to me, with a story that has you hooked from the beginning and gut wrenching decisions at the end.
So, as an overall IF game, compared to most games in IFDB, Choice of the Ninja is high quality and worth playing, but compared to other commercial Choice of Games stories, I don't recommend it unless you're playing through them all.