Outstanding.
I've been a fan of this series of games for a while now, and had been anticipating that you would continue to impress with the third. As you say, it seems like it's been quite some time since the last one. However, I was right, and it's been well worth the wait. This is excellent work.
The graphics are wonderful. They're even better than last time. The colours and style really add to the atmosphere of the whole thing. The way everything is laid out also contributes nicely, dragging you into the story. It all gives it that great science-fiction feel. Talking of that, the plot is a big plus, especially in comparison to your average flash movie. I'm definitely looking forward to seeing how it'll progress, now more than ever.
The background music is very fitting too, and was never a distraction. The sound effects are also good. I think the last thing to say here is how effective the system of having action interspersed with areas of exploration is. It makes you wonder what's round the corner. The varied game play required for the periods of action is also a plus.
About the only thing that bothered me at all was how it seemed a bit short, but I suppose that's unavoidable given the nature of the game and how you've got to try to keep the size down.
Great stuff.