Truthfully the most innovative Legend of Zelda was Link to the Past.
Majora's Mask was good, but about 50% of the game was gimmick and side quests. Yes, they were fun side quests, but it did not feel like a complete package. And it is not nearly as good as people remember it or desire it. I think people really enjoyed the atmosphere of that Zelda game and felt it was darker but with the same Zelda charm.
As an overall experience I believe Twilight Princess is every bit as good as Majora's Mask, but no where near as complete of an experience as Ocarina of Time, although it did do some things better. (I felt Twilight Princess had a much better pacing, pushing you through the first 1/4 of the game until you have a good amount of story and items and then opening the world for you to explore. )
But Link to the Past introduced the more complex puzzles, changing world (light/dark) interactive environments and puzzles...and basically is still today the standard Zelda falls back on...it is the most playable and innovative Zelda game.
I also don't feel Zelda has any threat of becoming like Star Fox. Star Fox is a niche shooter brand that has tried several attempts to branch into different styles of games to give it more appeal, but in the process hurt the overall feel and appeal the originals had. Zelda is not a niche title and as it expands it is not doing so to try to appeal to a wider audience, but just continue to provide the engaging experiences that people have come to expect from Zelda...but the truth is, everyone gets a little happy and joy when they begin to play a new Zelda adventure....just like the same joy people get from starting a new Mario adventure.