Finished the game a few days ago, and have been mulling over the plot. Some aspects of connection to the series 'canon' are clear, and others not so much.
In a way, I feel like SS and TP form their own story arch, just like OoT-MM-WW form their own story arch. Aside from obvious overlaps like naming conventions, think of the nuances in their relationship:
- In SS, the Master Sword is placed in a temple just outside of the forest, in the Faron province. In TP, the Master Sword is located in what used to be a temple just outside the forest, in the Faron province.
- In SS, Link gains the symbol of the Triforce on his hand, indicating his status as the goddess' chosen hero. Since he stays on the surface with Zelda, his bloodline presumably passes on. In TP, Link begins the game with the Triforce symbol already on his hand. The fact that SS Zelda mentions that one person is not allowed to hold the entire Triforce lends reason to the split authority between Link, Zelda and Ganondorf in TP.
- In SS, there is a city in the sky. In TP, the characters reference a city in the sky.
- In SS, you find remnants of the old, robotic civilization. In TP, characters make reference to an ancient civilization with advanced technology.
- In TP, a light guardian imparts the story of the 'dark interlopers', magic users who sought the power of the Triforce and were banished to the Twilight Realm. In SS, Demise is the leader of a group of magic users who seeks the power of the Triforce. It's entirely possible that remnants of his faction tried to continue his efforts.
Until I reflect further, it just seems that SS is more of a set-up for TP than OoT (especially since the connection between TP and OoT is just so nebulous), even though SS was apparently supposed to explain the foundation of OoT.
Certainly, SS makes clear where the "Hylian" race derives from, and cleverly grounds every major villain's motivation (i.e., Demise's curse); and I can even believe that the Sealed Grounds becomes the "Temple of Time" in OoT (there do seem to be some structural similarities, and obviously the Master Sword lays dormant behind a big door). But I just wonder now if SS and TP are pushing OoT out of its central position in the Zelda canon, much like OoT and WW derailed some of the plot significance of AttLP.
Granted, that also depends on whether you think the timeline is meaningful, and the degree to which you think Nintendo really is just "retelling the legend."