Just because a feature is "needed" doesn't mean that its inclusion isn't innovative. There are a lot of people saying that Zelda "needs" certain things in them to become more innovative; does that mean that if they did get included, they wouldn't be innovative? No, not really. Say what you will, but Gen II really added tons of things to shake up the experience. And where you see "filler" in Kanto's inclusion, I see extra content to explore and see how things changed between the games. And comparing HG/SS to OoT 3D is kind of blind; while OoT 3D did very little to change the gameplay experience, HG/SS still changed up a few things and added several other bits of content.
So, yes, it was still the most innovative generation, despite what you may think of the games themselves. Though do I think Gen VI can be just as innovative? ... no, because there was far too much in Gen II, but Gen VI still has a chance to be more innovative than the last three generations. Which is, not very. But no one can judge until we play the games for ourselves, so we shall see. I'm hoping they turn out well. Only nine more days...
EDIT: I do want to note I'm not criticizing anyone for not liking the games, I just find it difficult to believe that the games can't be considered as innovative as they were.

