There are a lot of different ways to do 3D these days. With "Man of Steel", we did everything like a normal 2D 24fps film and the 3D stereo conversion was handled by an outside specialist company. This kind of post-conversion can really be a mixed bag depending on so many factors, but if done well it can be a less involved method of making a stereo film, though it'll never achieve the same level of immersion you get with a film that's made from the ground-up in stereo like "Avatar", "Life of Pi" and "The Hobbit." But that heavily integrated pipeline is really expensive and can create lots of difficult problems to solve.
The post-conversion method is very labor intensive but not as difficult. It involves having an army of 2D artists and technicians cutting out objects in the shot and moving them into Z-space (ie camera depth). The downside is that you're essentially working with a photograph, so you have a limited amount of information to work with whereas a full 3D stereoscopic shot is literally a perfect view for each eye, so there's proper parallax from the camera to infinity. The post-conversion artists have to fake this and when it's done well it's pretty convincing, but when it's done poorly it'll give you a headache.
The two most common reasons for headache inducing stereo conversions are budget and time. Some films are rushed to the theaters and they don't give the proper budget and schedule to the conversion so it gets completed but not to high quality. Also there are sometimes cases where it's decided at the last minute to do a 3D conversion, so again there's not enough time to do it properly - this was the case a few years ago with "Clash of the Titans", with the decision to do a stereo conversion literally a couple months before it was scheduled to be released in theaters because "Avatar" had just killed the box office.
ETA: For the record, it was decided that "Man of Steel" would be a stereo film back in mid-2012, so my guess is that the conversion is top-notch.
