(Here be spoilers.)
This wasn't a bad film. It wasn't a very good film either.
The problem is, there was no way for me to connect with the main character. There was a conflict and humanity's survival is at stake. I care about humanity. But instead, the film was more focused on Tom Cruise's character and the way he reacted to his situations. And frankly, he wasn't interesting enough for me to care about. I think this was because he didn't really have individual goals of his own. He was just some dude. And then, we find out he's not just some dude, he's a super special awesome astronaut dude. And we're supposed to care. But it's hard to care because he just isn't interesting.
Probably what's even worse is the villain. If you want to make a good movie about good versus evil, you have to have a compelling villain. You have to at least semi-understand the motivation of the villain. Some good example of great movies that have great villains: The Preacher from Night of the Hunter (motivation: greed, lust, religious fervor), HAL from 2001 (motivation: can't let his job be jeopardized), Khan from Wrath of Khan (motivation: superhuman supremacy). "Sally"'s motivation is never really explained. Maybe it's just a malicious device made for tormenting other alien races. Maybe it's just trying to help out its creators who are dying on some other far away galaxy. The movie never really attempts to explain. And I really don't mind movies that have ambiguity to them. I just dislike movies that have no meaning.
So in the end we have: A protagonist we don't care about and an antagonist who is too vaguely conceived to hate. Whenever Tom Cruises character dies saying "Fuck you Sally!" he might as well be saying: "Who gives a fuck, Sally?"
The story in and of itself consisted of a lot of science fiction clichés (main character is a clone, unknown alien manipulating humanity for its own purpose, etc.) That's not necessarily a bad thing, but coupled with the blandness of the characters, the story is ultimately uninteresting.
I will say this: the CGI is well-done. But in the long run, it will be out dated. Whenever people see this movie in the future, they'll think: "why did people even bother giving this movie 267 million dollars plus? "