Demise's realm could've used a series of Dark Link battles to make it seem like a never-ending source of doom.
I don't agree with this. What would the Dark Link battles have added to the story at all? This is supposed to be the final fight between the Hero of the Goddess and Demise, the bane of Hylia. Adding in Dark Links would have needlessly distracted us from the true terror. Besides, Demise created this real specifically to have a one-on-one duel with Link with absolutely no interference from outside forces; Dark Links would have gone against this. Demise's final battlefield was perfect the way it was.
The Past could've used more backstory, at least three dungeons exclusive to it, and a dungeon that is linked to the present sort of like a throwback to Oracle of Ages, but far more intricate and CHALLENGING.
I... DO agree with this, though, at least partially. After further reflection, I think this might have been a really cool idea. While I think we still got a fairly good idea of what happened due to the whole of the Lanayru Province, it still would have been even cooler had we seen the attacks happening in the Faron and Eldin province around that time period as well. Though I'm not really sure how they would have integrated that into the game, and I'm still happy with what we got.
Moving on to other games...
I think the sunken Hyrule was far underused. I think we would have had an even greater sense of sailing atop a dead world if we had seen more of that world under the waves, instead of just the castle and Ganon's tower.
The Snowpeak region in TP was also greatly underused. I wanted to explore a vast region perpetually covered in ice, like the Phendrana Drifts in Metroid Prime. But instead all we got was a straight shot to the mansion.