This confirms:
Link and Yoshi are working together
at some point in the storyline.
This confirms:
Link will fight a Shaydas at some point in an arena that looks very much like something out of TP. This may be a representation of the Kakariko underground.
This confirms:
Yoshi will encounter a Trowlon at some point in a lush, forest-like area. Possibly Yoshi's Island?
http://www.smashbros.com/en_us/gamemode/modea/modea10.html
This confirms:
Link and Yoshi are working together, possibly in a desert area. Link (maybe Yoshi as well?) seems to be in some sort of desert temple
at some point in the storyline.
Sooooooooooooooooooooooooo...
Well, it really depends on which princess you
don't rescue. If Zelda is trophied by Wario, Link will at some point get word of it and do his d@mn best to save her @$$. This appears to involve a desert and a Kakariko-lookin' place. How does Yoshi play into this? Well...Yoshi's Island was Subspace bombed and only one Yoshi survived? The Ancient Minister (or an evil minion such as...Wario, maybe?) has stolen all the Yoshi eggs? A combination of the two? The pair meet up and join forces, a pair of green heroes who don't ever talk. But how do the pair meet up? Well, since Zelda has been trophied and all the Yoshi eggs have been stolen (I'm choosing this option 'cause it seems more likely for my theory)
by the same person (Wario), it's possible that they meet just before a fight with Wario, join forces, and @$$-pwn him. Then they head off to confront the rest of the Subspace Army.
But...
If Zelda is rescued from Petey, if
Peach is trophied...
...that's something entirely different.
Link is riding Epona across Hyrule Field, maybe soon after the ending of TP. The Halberd flies overhead, spilling Primid juice across the Bridge of Eldin. Link is shocked and gallops off to confront the Primids, but an orange magical barrier is thrown up. Link wheels around to find...holy crap! Ganondorf! He is holding his sword in one hand and a trophy gun in the other. He fires the gun, but Link easily dodges and launches himself at Ganondorf. You fight Ganondorf on a Hyrule Field stage. When you beat him, he vanishes, laughing, and a Yoshi egg appears where he was. The egg hatches into a baby Yoshi, which you then have to feed. You carry it like an item to the Bridge of Eldin and feed it a few Primids. The baby grows into a fully-grown Yoshi and together, you fight the Primids. You join forces and head off. Throughout the course of Link's storyline, you fight Ganondorf many times before having a final showdown with him. You also encounter occasional Shadow Links, Ironknuckles, etc. You don't meet up with Zelda, 'cause she's either with Kirby or Mario, depending on how the
beginning played out.
So...yeah. What'd'y'all think?