I completely agree. The movie was absolutely beautiful, but the plot towards the end seemed really forced.

Spoilers:

It seemed to go downhill as soon as Elizabeth found out she was pregnant and escaped the room she was in to have that machine remove it. Shortly after, Janek is telling Elizabeth about the planet being a research station without acknowledging what happened to her at all. From what I can remember, not one person mentioned it. She even had to knock out people to escape the room, if I remember correctly.