The thing about these localization debacles that really gets me is that people seem to think that English is the only language things ever get changed or "censored" in, and that Japan is some magical land where everything is permitted. But things get changed or removed in the transition from English-language media to Japanese all the time. A particularly famous example is cartoon characters with only four fingers on each hand. This is an incredibly common animation trope in the West. In Japan, however, four-fingeredness has a deep cultural association with the Yakuza (and subservience in general) since Yakuza members will cut off their pinky fingers as a way of showing subservience (a tradition that dates back to feudal Japan, since a person missing their pinky has less control and grip on a sword). So something as innocent (to us) as a cartoon character with simplified hands has a nasty connection to something criminal and unpleasant in Japan, and a number of Western cartoons have had their hands painted over or digitally altered to have five fingers in Japan.
A good example of this kind of localization in video games is in Banjo-Tooie. In one level of the game, there's a group of pigs who went swimming in a pool polluted with some kind of toxic waste, and as a result, one of them has grown an extra arm. Silly and funny if you live in the West, but in a country that's dealt with the effects of nuclear fallout in populated areas, far less so, especially in something intended to be a reasonably lighthearted family game. In Japanese, the character's extra arm was removed and the mutation references were cut. Not surprisingly, something similar happened in the Fallout series--you can't detonate the disabled nuke in Fallout 3 any more in the Japanese version, since something like that would be incredibly uncomfortable there.
Heck, there are even non-Japanese examples out there. There was an episode of the children's cartoon Peppa Pig that outright wasn't shown in Australia because it was about how you shouldn't be afraid of spiders. In the cartoon's homeland in the UK, that's a perfectly acceptable moral since most spiders you'll find there are harmless critters who'll eat the annoying pest bugs in your house. In Australia, which is home to an incredible number of deadly spider species, you don't want your children to run around playing with any old spider they come across.
Different cultures consider different things acceptable, and more often than not, you're going to run into one or two when you're translating or porting things across country lines. Sometimes they'll just look funny to outsiders--for example, giving people gifts to befriend them in the Harvest Moon series sometimes looks a bit bribe-y in the West, while people in Japan literally give more gifts than any other nation on Earth--and sometimes it gets too uncomfortable--like anything skeleton-related in China, where it's considered in EXTREMELY poor taste to defame the dead. And if you want to make a work considered acceptable in a different country, you have to adapt.