Besides the suit I'm pretty sure one of the MoS trailer hinted at Superman not being trusted by people like he usually is which is also happening in the new comics. There was also the whole being captured by the military thing I believe is in one trailer which happened at the end of NuAction #1 and carried on in NuAction #2.
But that's not unprecedented in earlier Superman tales. There was a subplot in season 1 of Lois and Clark
about a government agent investigating Superman as a possibly hostile alien. There was General Hardcastle in an episode of Superman: The Animated Series
, the whole Cadmus arc on Justice League Unlimited
, the vigilante-registration/Civil War
knockoff storyline that Smallville
did in its last season, etc. It's got enough of a pedigree, and is enough a part of the modern zeitgeist for alien-on-Earth stories and superhero stories, that the movie and comics could be building on it independently rather than one being directly inspired by the other.