Yakuza 3 remastered took out a Substory that was deemed transphobic. I'm playing Yakuza 4 now, And one of Tanimura's sub stories has him team up with a transgender woman. In fact, a lot of transphobic dialogue was excised from the remastered versions. In fact, Kiryu and the protagonists don't think any less of someone for being trans. More @Wikipedia
Hover over any link to get a description of the article. Please note that search keywords are sometimes hidden within the full article and don't appear in the description or title.