I've thought for some time that both Mario and Zelda have been on similarly mixed up trajectories in how they have transitioned from generation to generation. A theory in THREE ACTS
Nes - they both came in, birthed from pretty much opposite philosophies (linearity < -- > exploration) as I've seen stated somewhere whatever ideas they believed didn't fit with one, they repurposed for the other. Both had weird follow ups, Mario being quicker to action got 3 out while Zelda doesn't have a matching move.
Snes - both refined and exemplary additions to their respective series.
N64 - both nail the transition to 3d, Mario being the perfect introduction to the analog stick, and Zelda giving us z-targeting. Mario has no follow up yet, while Majora's Mask is a perfect compliment to Ocarina.
GCN - Here's the big misstep. and where I believe history should retroactively change to reflect the right game at the right time. Both Sunshine and Windwaker while being great titles, do not fit on the cube. After the spaceworld demo, Twilight Princess was the game that should have come out (and eventually did, but only technically as it was a Wii launch title). Galaxy, while being a great Wii title, could have simply been a cube game, the waggle and motion parts weren't essential and had they made Galaxy the follow up (here's where you're mind is blown)
Think of the progression, after Mario 64, to go directly to Galaxy, and then when the Wii comes out, and it's party games, and colorful fun, Sunshine is a perfect fit, Yoshi returns after a two game absence rather than appearing and disappearing, and if they then followed it up with Galaxy 2 giving players a space-break before an even bigger helping of planet hopping Yoshi having action.
Back to Zelda, you have Twilight Princess be the cube title, then on the Wii you do Wind Waker, the fun, summery, colorful title, the Wiimote being a perfect fit for the titular wand, and then you follow that up with Skyward Sword and you a more logical progression of cel-da back to back rather than flop-flipping between styles.
Mario 3d World and Link between Worlds recently came out and have respectively garnered praise as 'best in a while' titles, I don't disagree with the sentiment, though I wonder if that's due in part to both series simultaneously taking erroneous left turns when all they had to do was drive straight.