The biggest issue here is Thor. More specifically Asgard. It played out in the comics with Thor coming to an agreement with Iron Man (after slapping the piss our of him at his leisure) where Asgard is seen as a unique political entity and therefore not subject to the Registration Act, but when you have a world inhabited by gods that could tear the human race apart 17 times before lunch without breaking a sweat, man made laws are impractical and unfeasible.
In reality, the biggest problem with Civil War is that Iron Man was clearly the villain. It came down to bad writing. Instead of two diametrically opposed sides both with valid points, it turned it Captain America being the good guy and Iron Man (and the pro-registration side) turning into cartoonish villains.
The individual that came off the best out of the whole event was Thing, with his "Fuck this, I'm moving to France!" attitude.