The worst thing it could have done it avoided... (Spoilers)
It didn't turn the government/terrorist Coalition Against The Borg into the good guys. They are a bunch of scared and clueless people doing what scared and clueless people do. Reaction with violence and hatred. OK, One might have wished that Freeman's and Bethany's character knew better and actually talked to the AI before trying to destroy it, but just because they're scientists doesn't mean they have to be flawless. At least they're much more competent than Prometheus' "Scientists". I hated those guys, but - that's the point. In the end - they were wrong. Which is a much harder ending to pull than "they were right all the time and the evil computer wanted to kill us all!" In the end you didn't stop the Borg invasion. You killed the smartest being ever to live on Earth and just wanted to help. Maybe the message was a bit unsublte in the end? But after spending so much time with the Resistance movement, I think the movie needed to make clear they were wrong.
Talking about the Computer. The biggest wasted opportunity of the movie is their silly focus on "Is it Johnny Depp or not?" Who - at this point gives a damn? The question is: is it sentient and does it mean harm? Not "Is it Jack Sparrow"? The whole movie could have massively benefited from dropping the "uploading his mind" angle completely for a version of Person of Interest's Machine gaining sentience on its own. (A certain Christopher Nolan was executive producer so don't tell me nobody considered that). That would have been better.
Still. It's not as bad as I feared it is after many bad reviews. It's not even meaningless, as Charlie Jane thinks it is, even though I get that. It's far from being as good as it wants to be. Or could be. But it's still not bad. It really isn't.