I did the same thing, but FYI, the flying amoeba is completely harmless, have a heart and don’t hurt them.
You’re right that it’s a big improvement. I enjoy the puzzly bits and the platformy bits, the long jump makes them substantially less annoying than your average first-person platforming, even though boosting into an angled surface often makes you bounce off unpredictably, catapulting you into the void if you’re not careful.
What I’m a little disappointed with is that they dialed down the alienness of it all. Some parts of Xen are like lush, vibrant jungles, with woody, leafy trees, shelf mushrooms, and chirping creatures in the background. Then the factories are all metal and glass, rectangles and cylinders, button-operated elevators, and so on. The flesh tunnels are a step in the right direction but overall it feels far too familiar, like a comfortable James Cameron-esque fantasy of an alien world rather than something that feels like an effort to be alien. HL1 Xen did a lot better in that regard.
Also, the Gonarch fight was drawn out over far too much of the game, and I kept wishing they would just let me kill it already instead of having to run from it the whole time. Overall the setpieces are extremely impressive though. There’s a bit that comes after escaping the factory that I especially liked.