They aren't doing the 3DS version, but they are still doing stuff with the franchise.
Skylanders Giants was confirmed for Wii U last night, and around the same time, n-Space was confirmed to be making the 3DS version. So where does that leave Vicarious Visions, the developers of Skylanders 3DS?
An Activision rep told us Vicarious Visions is still working on the Skylanders franchise, and with their past output on Nintendo systems, it is likely they could be working on the Wii U version, which is still pretty hush-hush at Activision's booth despite an executive saying it is coming.
Of course, they could also be working on more iOS titles. I assume we will find out more in the coming months about the status of Vicarious Visions and Skylanders on Wii U.