According to Avalanche Studios chief creative officer John Blackburn, the 3DS just isn't powerful enough to work in a similiar way to the Wii U game and so his team built a handheld game featuring mini-games.
"The 3DS is a very different experience," Blackburn told Destructoid. The memory can't handle all that stuff, so technologically we couldn't do the same thing there.
"It's more of a game you expect on a 3DS: You build teams with characters and they each have a mini-game that comes along with them. You can go and build out the different play fields that you'll go through with your team, so there is a strategy component when you play with someone else."
So while there is still a building element like in the console versions, it seems that the likes of Sulley, Jack Sparrow and Mr Incredible will have to complete mini-games to progress.
The price for Disney Infinity 3DS Starter Packs at many stores is £54.99 which is cheaper than the Wii U version.