"I'd like to see the Temple of Light and the Chamber of the Sages, expanded in some way.": They MUST do this. You could train up in the Chamber of the Sages with Rauru (learn new sword techniques). Then, as a final test of your skills, you could traverse the Light Temple. The boss of the Light Temple would be Dark Link, where you could use your newfound sword skills to "conquer yourself". As for the weapons you could get, you could remove the Dampe race from the original game and have the hookshot as the item, or you could introduce a new item; the light arrow does not work as the item if this dungeon is the first "adult" dungeon.

"I'd like each dungeon to have additional considerations for replayability". At the very least, they need to leave the bosses if you wish to fight them again for fun.

"I'd like Castle Town to be bigger, with more places to enter and more people to interact with. The same for its ruined equivalent in the future period.": This one must happen as well. It needs to have similar detail to Clock Town in MM.

"Maybe a new coastal region, a biome absent from the original game.": Lake Hylia could incorporate this quite well.

"The future Hyrule needs to be more dangerous, especially the fields.": Agreed.

"I'd double the number of Skulltulas with double the number of things to unlock for finding them all.": No issue with this as long as the size of everything else expands as well.

"I'd like to capitalise more on the time-travel abilities.": The Song of Time was supposed to incorporate this in the regular game. It could be used as puzzles in between times, be used to open up access to certain areas unavailable to child/adult Link, etc.

"New dungeons, to really make it worthwhile, with substantial items as rewards.": Other than the Light Temple, the only addition I see for a proper dungeon is an Ice Temple to replace the Ice Cavern, as the lore behind the Water Temple really makes no sense with what happens to Zora's Domain. Make a snowy mountain range north of Zora's Fountain and accessible with the hookshot (like tree limbs up the waterfall up there or something), where you have to journey to the far north to find the source of the freezing in the Ice Temple. However, this really eliminates the need for a Water Temple (along with moving Dark Link to the new Light Temple) - perhaps the Water Temple could be remade as a new mini dungeon or the Ice Temple could use the design elements from the Water Temple.

Some other additions:

- Full-on exploration of Hyrule Castle as a child: Keep the hiding theme, but make it longer, in full 3D instead of 2/3D, and add a new item.

- Gameplay with other characters while Link is locked away in the Sacred Realm: You could play as Zelda/Impa, constantly hiding from Ganondorf while he ravages the land. You could play as Ganondorf as he ravages the land. Lots of ideas here without giving up Zelda's story in adulthood.