I might get hate for this, but I would not like for any connection between the two where you have to get all the unlockables. I think it would be best if you can unlock all the stuff without cconnecting between and get it on your own for the Wii U. As for the 3DS, you can unlock everything on your own, or you can use street pass to get unlockable stuff. All I know is that you can transfer customized characters to the Wii U, and because of that, I hope the 3DS can be used as a control. Mostly because I'd rather use one control for both instead of having to get used to two. And if I can use the 3DS as a control, I can go to tournaments for the Wii U and play without having to practice on the Wii U (this could only work if the Wii U and 3DS version will have the same game mechanic [I think they do, but I am not sure]). That would also depend on how different the two are. Since people will want fair stages (battlefield and final destination), I am pretty sure there won't be much difference.
with them saying that Wii U will be limited to the 3DS in content, this makes sense to me.
I don't think it will be limited in content because of the 3DS. The only limit I can think of is characters, and I think Sakurai wanted to add a certain limit to them regardless of what the 3DS can handle.