I'm not sure... It seems to me that Super Mario Galaxy didn't make huge strides in terms of innovation. For the most part, it stayed within the safe confines of the series; Little if nothing new was introduced for anyone familiar with Mario Sunshine and Mario 64. However, it still managed to be an amazing game. If it wasn't very refreshing, it was a great romp through a familiar role since it retained the same charm and spirit present in Mario 64.
It seems to me that Wind Waker and especially Twilight Princess failed to capture the Zelda essence, whatever that is. TP was just totally outlandish and it felt massive and empty. Maybe Nintendo just needs to get their mojo back, though I'm not certain where it went.