There's a male and female baby for each family. If you get a Mame-Family baby, it'll always grow into one of the Mame-Family characters, and so on.
There's a cooking feature, which is pretty cool. It's longer-lived than the English versions, which gives you longer to build up its GUTS Points.
Instead of just seeing pictures with the letters and such, you get newspapers and letters with actual text. It's all in Japanese, though, so if you can't read Japanese, it's not much help...
It's also got an extra family of characters you can get that aren't available in the English V4.
You can't choose when to go to the school, the teachers just come to you at certain times throughout the day. It's the same with the shopkeeper, he comes to you throughout the day to sell you items/food/cooking materials, there's no shop for you to go to.
There's also no pause feature, you have to pause it with the time-screen trick like on the vintage models or removing the battery.
Umm... I think that covers most of the main differences.