I do have an idea for a more... realistic (?!) method Brainiac can use when it comes to stealing cities.
Have him capture cities as they are, sans the shrinkage. He places them on the surface, or inside of his planet-sized vessel (think Cybertron/Death Star). His goal is to re-populate his empty home world. The vessel IS his home world, and he's an advanced AI synced to every computer there.
Barring that? Go the "Reaper" route from Mass Effect. Instead of stealing cities, he harvests genetic material from across the universe for some reason or another. This ties into a theme from MoS.
I like that first idea