I think this thread has turned into a "which interests me the least" thread. Even if we were being objective though, I think the Wii series would still be considered worst. It succeeded due to a fad. It wasn't very well realized, honestly, and could have been way more than it is. However, as much as I absolutely ADORE Star Fox, I do know that it also suffers from being less than it could be, so it deserves its second place as well. As far as I'm concerned, the ground exploration in Adventures was fantastic and a needed expansion to the series, but the space combat in that game was unforgivable, and pushed to the side, which wasn't okay at all. Still love the game though. And of course 64 was the best example of the spaceship dogfighting gameplay. Assault was where it all went wrong, because it tried to blend ground and air combat together, and failed pretty miserably. It was an okay game, but it pales in comparison to 64, and the ground combat was better in Adventures, and exploration was a complete non-factor in that game. Then Command happened and...ugh...that game was worse for the series than Other M was for Metroid. The series could use a complete reboot, and would be the first Nintendo franchise to truly get one. So in the sense that it's Nintendo's only series to ever need a reboot, it would definitely deserve second place.
That said, perhaps a series that needs a reboot even more is F-Zero, so I personally would say that is currently the worst. Even Miyamoto doesn't know what to do with it.
As for Animal Crossing getting 3rd place, that's utter bullshit. No reason for that. Even if you don't like the series all that much, it's the best game out there of its kind.