I disagree with you that “Aliens Vs. Monsters” had “nothing else objectionable” besides some mild violence. I took my daughter, Amita June, to see the movie, and she was really upset at the kidnapping and imprisonment of lead character Susan. I didn’t have much to say to her — I find the idea that the US government puts people in secret prisons just because they’re different pretty disturbing too. (Yes, the Missing Link does cause chaos on Florida beaches, but many of the other characters in prison didn’t do anything except be “monsters”.)
This isn’t just a fine point that young children and over-sensitive lefties like me would get up in arms about. It’s integral to the plot of the movie. Susan gets really upset, too: she cries and objects during most of her imprisonment. Worse, the perpetrators never pay a price or even show remorse for her unfair treatment. The only way she eventually gets free is by going into a dangerous battle (and it’s not clear that she has a choice).
The fact that Susan later makes friends with her fellow detainees is cold comfort; although the general eventually comes back to save her life, I found the whole thing really uncomfortable.
Maybe older kids will understand the hommage to other sci fi movies — that a “secret government program” holding people against their will without having committed a crime is pretty standard fare — but younger kids will have problems with it. And the fact that those same captors end up being “good guys” in the end is not much of a help.