Now that we are the proud owners of both Doctor Who games, apart from reducing a lot of arguing over who's turn it is to play in our house, we can see the big difference between the two games. The first game for DS is a Professor Layton-style puzzle adventure which is suitable for older kids and the the Wii game is an actiongame more suited to younger kids - although there was a joke by the doctor in the first few minutes about the staff canteen in the space ship being closed which had me chuckling (and the kids looking at me like I was mad).
I think if your kids are older, in the 10-12 age group, they may find the Wii game a bit easy and I would recommend the DS game for them, but I think the Wii game is perfect for ages 7-9.