Link from OoT/MM is the Hero of Time, and the Hero of Winds doesnt feature in Spirit Tracks or Minish Cap. But I get your point, but im pretty sure the Hero of Men your on about didn't have a cap, but SS Link certainly does.
I like Ganondorf, but I dunno how he'd fit into this timeline wise? Malladus was cool, but he turned up between PH/ST didn't he? Mhmm, I wouldn't mind a new villain. A proper jerk please.
We didn't learn about the Spirit Pipes straight away, so dont jump ship quite yet. Makes no difference to me though, if the odd game is minus an instrument.
I guess the preview art got everyones hopes up for a TP sequel. To be honest I was disapointed at first too, but now I really do dig these new graphics, they are just stunning.
The concept logo was amazing, the current one seems like a Paint job. To be honest, the logo is the only thing I dislike about SS so far. The rest of it seemed pretty amazing.