I just finished the game last night. These are some of my random impressions.
1. I believe that TP reconciled the different placements of the Master Sword in aLttP and OoT. In aLttP, the Master Sword is in the Lost Woods, and in OoT, it is in the Temple of Time.
IMO, TP reveals that these two locations are one and the same. The Temple of Time is a projection over the forest, with the Master Sword being located in the exact same spot in both settings.
Also, the gripe about how OoT's Temple of Time had no associated dungeon is explained away by TP. TP tells us that there was always a dungeon behind the Temple of Time (through the stained glass window); we just couldn't access it in OoT.
2. It seems that Nintendo went out of its way to ruin the continuity it was developing with OoT and TWW. When you open the Twilight Mirror for the first time, why are there only 5 sages (rather than 6 or 7, depending on whether you count Zelda)? Why is there no foreshadowing to TWW?
And wouldn't the game have been so much better if they had recreated the inside of TWW's Hyrule Castle in TP (the boss room KIND OF looks like that room, I supppose) Or if Mother and Child rocks were huge, towering rocks that could later form the Mother and Child Isles in TWW? What about bringing back some obvious descendants of characters from OoT (besides just the Postman) and some obvious ancestors of characters from TWW? Etc., etc.
The biggest complaint in this department, however, is the lack of nods to OoT. I can accept that maybe TP and TWW are on different timelines, but just as OoT's story is widely known in TWW, it should be in TP. I don't even need a long cutscene; just give me stained glass windows with sages on them or something. I need some assurance (aside from Aunoma's word) that the game I'm playing comes directly after OoT. Especially if TP comes a mere century or two after OoT.
3. Didn't it seem like TP "jumped into the story" a little too quickly? Within 30 minutes of playing, people were already calling Link the chosen one and a legendary hero, and he got stuck in some bizarre twilight realm. Part of what made OoT so great was the slow pace at which the main conflict unfolded.
4. Does TP's definition of "shadows" as being part of the Twilight Realm shed new light on OoT's Shadow Temple? Could it be that all the invisible things that you needed the Lens of Truth to see (or to see through) were really just parts of the Twilight Realm?
Also, there are a lot of whispering murals (?) on the walls of the Shadow Temple which talk about the bloodlust and greed of the Royal Family. Could these whisperings be coming from the exiled members of the Twili tribe who bear a grudge against the Royal Family for banishing them (and/or their ancestors)?
5. I hate to say it, but the ending was atrocious. I kept waiting all game for something to explain TP's connection to OoT/TWW, or at least some more exposition about the Sacred Realm and old Hyrule. Instead, all we get is a throwaway line from Ganondorf about light and shadow, and then Midna turns into a Zelda lookalike, and then she leaves into the Twilight. Who really cares?
6. I think the question of where TWW's Rito came from is answered in TP: the Ooccoos evolved into them. In terms of where they got their Postman-like qualities from, well, maybe an Ooccoo mated with the Postman.
Anyways, that's all for now. Feel free to comment on these or add your own random thoughts.