The GamePad for Nintendo's upcoming console includes near-field communication functionality, but studio head Paul Reiche believes the portal will remain a "fundamental" part of the franchise.
He told Digital Spy: "The problem is, if you look at the NFC, it's in the GamePad, which is really convenient if you want to do the traditional 'swipe your card', but trying to set a toy on there, it slides off.
"At first, we looked at the NFC feature before we got the hardware specs and we were, like, 'Uh-oh, now everybody can do this'.
"Then we saw the Raving Rabbids and the video that showed them putting the toy on the GamePad."
Reiche added: "Unfortunately, [Ubisoft] dropped that feature, and I think for potentially the same reasons, which is - for an ongoing game mechanic, it didn't seem well-suited, as you are holding the GamePad."
For Skylanders Giants, Toys for Bob will be releasing a range of 'LightCore' Skylanders toys which light up without the need for batteries when near the portal.
Reiche added that the developer is interested in exploring this further in the future and using NFC in new ways.
"If you take any of our new LightCore toys - any of our toys that have lights - and if you take them up to any NFC field, they'll start to glow.
"There's definitely a relationship between them in the future that we could use. The ability to take your toy into your mobile and play with them somehow seems really compelling, but we don't have that yet."
Skylanders Giants will be available on Nintendo Wii, Xbox 360 and PlayStation 3 from October 19 in Europe and October 21 in North America.
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Watch a trailer for Skylanders Giants below: