I don't know how to describe it, but they both have the same feel to them. Karakuri Circus is about a boy who's travelling around, running away from an organisation after his money that was handed down to him from his father. Fullmetal Alchemist is about two boys travelling around the country, trying to find a way to get their bodies back.
They have a similar vibe and both are adventure shonen. They also both have quite a story hidden behind their battles between silly yet creepy carnival-like foes. Will humanity survive or have their last laugh?
While not anything alike in plot, both shows feature mystical puppetry as their main gimmick. They both have highly stylized characters, both feature suspense, mystery, and violence, and both will likely not get the attention they deserve. They're also both an interesting mix of silly and violent, which is a fun combination.