I think the core story could have been interesting, that the main character learns he is a clone working for the bad guy, and I agree, they could have explored this a bit more, but they were too busy making it an action movie.
Here are things that I think are stupid:
1. An alien entity powerful enough to shatter the moon, that can make killer robotic drones, and is knowledgeable enough to both clone humans and erase their memories doesn't really need to go through the song and dance ruse of making the clones think they were saving humanity. It is a huge waste of effort to set up these people in ergonomically perfect housing just to do maintenance work. We don't have a clear sense of why the "Tet" has arbitrary limitations.
2. How is it directly converting the world's water to energy? If we assume it has the technology to do mass to energy conversion, the amount of energy it would gain this way it phenomenal -- it was actually draining the oceans! Given the abundance of energy at the Tet's disposal, we again wonder as to its limitations.
3. I am doubtful that any being with this level of sophistication, that can actually suspect and detect possible duplicity in humans, would allow itself to be easily exposed to danger. OK OK, I will grant this one, maybe it is just really arrogant and doesn't fully realize how sneaky humans are, despite being able to manipulate their brains.
I'm not even going into all the plot holes and and contrived plot points. I just find the whole setup for the story stupid. If the Tet is as powerful as it appears, it has little need of clones, and would hardly lack for resources. If it is as sophisticated as it appears to manipulate the clones and understands their needs enough to build perfect shelters for them, it wouldn't have the limitations it appears to have in terms of understanding and lack of information.
The story just felt really contrived the way it was done.