I would say DS > Gamecube >>> Wii
The City options for the Wii version were cool but at the same time, they didn't make it that much better. The gamecube version allowed for you to have a basement, which was awesome. I never had the Gamecube version but I watched my bf play it for a while. And there was a lot of content for a gamecube game.
Not to mention the fact that, in the GameCube version, you could unlock all kinds of full NES games you could play in your in-game house. That's how I first played many Nintendo classics, such as Wario's Woods, Clu-Clu Land, and NES Baseball. The DS version wins out on account of its portability, though.
I think the 3DS game will be my only retail game that I would want in downloadable format instead. I prefer physical carts and discs, but Animal Crossing is the kind of thing you want to jump into for five minutes several times a day, as a side dish to whatever 'main' game you're playing at the time, and it's cumbersome to carry around multiple games/cases.