While I will concede that Twilight Princess was a very bland Zelda game, I don't see Skyward Sword as being much better. The plot? Stopping an evil demon king from coming back to power. How many times have we done that now? Though, they did make some improvements since Twilight Princess, with gameplay and dungeons.
Now Majora's Mask was a Zelda game with some original ideas.
For its time, Ocarina of Time was an incredible game. I'd say the best game made up to that point. A huge technological leap, with a new story, new characters, great gameplay and the best soundtrack by far. It set the standard for the franchise.
Mario games are hit and miss. Some series seem to get more "care" than others. I don't think anyone would argue that the main games aren't good or great (Galaxy, Galaxy 2, etc).
Yeah, yeah, collect 3 things and stopping an evil force hardly makes something bland. Look at Halo 1, 2, 3, ODST, Reach. Covenant, covenant, flood, flood. Look at Assassin's Creed "I'm Desmond, I'm perpetually stuck in this dang Animus so long that my legs have atrophied from lack of use. Wouldn't you like to go back in time and stab people for hours?" "Why yes Desmond, I would." Didn't stop them from being awesome. Stale comes from overexposure, and wearing yourself out.
I played every 3D Zelda back to back on moving toward to Skyward Sword.
Skyward Sword is vastly different. It's not your regular "go to the mountain, go to the water place, go to the grasslands. Got it? Cool. On to the major plot. Ganondorf, har har, mastersword, kill, done." Instead of that wasted introductory space, the three elemental lands are strung throughout the game where your actions translate to a progressively transforming world. What you do directly influences and changes the landscape and the objectives within it. Side-quests, like Majora's Mask are fueled less by collecting (except the bugs) and more on exchanging words with one another. Your interpersonal relationships change and evolve, again--direct cause and effect. If you take your friend's mom's cash for cleaning her house, you can go back and he'll be screaming at her because that money was meant for food. Simple, but nice.
On a narrative side, instead of Zelda being a tool to progress you through your journey and Link a vessel for yourself, both were integral characters. There was a drive to rescue her, but from something she didn't need rescuing from--herself. She uses you as a guardian, but you never asked for it. You aren't a clever little kid thrust into an adventure where you are like "Sure, I'll kill this!" Instead you're a slacker who jumps into adventure because there is something of personal value that is at stake (ala Wind Waker). Characters could have been thrown away for one specific purpose (Majora's Mask, Ocarina, TP) but instead they had their own narratives, and powerful ones at that--specifically Groose. Not only that, but they had taken several epics all completely separated and had found a way to weave them into an intricate and cohesive plot. Great googa-mooga that's hard.
On the gameplay side, to say it had gone stale when we're finally given 1:1 control is absurd. (Whether you like that or whether that ruins your experience completely is another thing entirely, but it's not stale.) Who cares about the order you do things in, or the over-arching plot when
finally the biggest promise had been delivered--motion gaming that worked. Really, really, well. Sure most stopped caring at this point, including me. But onto the next point, it significantly changed the way puzzles are integrated. No longer were we regulated to pushing crates around for 10 hrs, because the items we used were evolved (for once).
Battles became strategic, and traversing the region was changed from never ending sea or dull land to brisk quick swoops into uncharted territories where you could launch yourself off of your loftwing, and quickly swoop back on if you so desired. Added to that the run function was something absent that created a monumental difference, at least, for me as I didn't have to hear him yell every two seconds as I rolled. It had a much needed flexibility to the generally stiff atmosphere that Zelda has.
The blending of over-world/dungeons was significant as it had finally fixed the sterile flow of "LOL HERE'S A BOX GO SOLVE THE PUZZLES IN IT". Instead, much like everything else in SS (except that tedious intro), the flow had been corrected giving us a vast playground that unlocked naturally as we explored. Much of the time it wasn't a boring "Here's your puzzle, now solve it" scenario staring you dead in the eyes.
I can guarantee that it wasn't stale so much as that people want it to change into something it's not. Which would completely destroy the franchise.
Bad timing + Wii MotionPlus + lack of a userbase that cares + no marketing = under-perform. Especially when the most bland entry (TP) sold more than previous titles. Games sell/give an impression off of image, marketing is very important. SS's problem was it marketed only to the people who would have bought it anyway and not to those who didn't even know it was coming.
t: I'm just explaining why I don't see it as stale in-depth to make my argument. In fact, besides dowsing (oh God) there was very little repetitious elements in the title. To me, most of our games we play are filled with repetitive drudgery. Perhaps because I am forced to play them all of the time. 
