I finished the game some time ago but I would agree with you Capt most of the first levels are very good and gets you really immersed. The zero G level was OK after I got the hang of it. The flying level really was poor imo. They could have done a better job of that.
Like you said with the spider robot it took me a while to work out you need to shoot it with the rockets I found on deck. Then with the big ship boss it didn't feel that a lot of thought was put into it. I think they must have thought lets put a big damm thing qt the end that you can kill fast if the TAC does not bug
But I will play the game through again later this year once we get better hardware out.