OoT 3D is being lifted by the bundle and was released far earlier in the year. Not to undermine OoT 3D's success - The fact that so many people are grabbing it and the bundle shows that people are interested in the first place. It has competition - SM3DL and Mario Kart 7, and a lot of people are still buying it (and I can't even find a bundle where I am - I'm not convinced the "limited" bundle is all that is causing OoT 3D to uprise) over or with those games.
But people are actually undermining Skyward Swords sales. not OoT 3D sales. It's selling at a faster pace than TP, and being (TP) an AAA title with name recognition as a launch title IMPROVES sales upon launch (and it was released for the Holidays just like Skyward Sword!). It's true that TP had a good 5 years to sell, though..and that's why SS is selling faster. I don't believe the game will die out near the Wii U's release and it's faster start will assure that it legs to 4-5 million anyway.
However, it's possible to go either way. We just have to wait and see what happens. The Oracles/Majora's Mask released late into their systems life cycles and didn't sell as amazing as other Zelda games in the long run. If Skyward Sword fails to make it to 5 million or even TWW numbers, it isn't anything we haven't seen in the past with the series anyway.