I think some scenes are modified.
They are basically the same, with just the smut scenes removed or altered. Therefore, I can't really say that this one's better that the other, but the adult scenes are really hot tho so if you are into those, then go for the yaoi version.
Thanks yous
Mature ver is better cuz there are some scenes (not sexy scenes) that was explained well here. Eg : How Shin's felt towards Wg
Is the shounen ai version the same as the yaoi version and if they are which do you think is better