It's hard to fault The Orion Agenda as far as its execution goes. It is well written, flows logically, has puzzles that make sense, always gives clues when you need them, and even has a storyline with a nice moral dilemma.
I have two issues with it, though. The first is that the world isn't really very fleshed out. The planet is described in pleasingly alien terms, but there isn't much to explore and examine as far as flora and fauna go. Most of the time on the alien world is spent trapped in a small village. The Orionites are very sketchily described, and seem to behave and talk much like humans. Their religion, which is important to the plot, is even sketchier. We have the names of some gods, some moral values, and a prophet. I'd have liked to see far more depth here. As it is, I didn't really feel immersed in an interesting alien world.
The second issue is that the game presents an interesting moral dilemma, but you're only able to make one choice. Wouldn't it have been more interesting to let either decision play out? The fact that doubts remain right to the end concerning the rightness of the decision sits uneasily with the fact that the player is railroaded into it.
So overall, this is a very competent game that offers a good storyline to follow and some well crafted puzzles along the way, but which doesn't feel like it quite does justice to its premise.