It is basically two games in one. The Clocktown/'sidequest' time loop game, and the traditional Zelda dungeon game. I tend to agree that the latter is mostly just not good. The dungeons don't improve with the existence of the time mechanic - in fact they needed to add a mechanic to slow time down because of how poorly the two designs mesh, which is kind of antithetical to the whole initial conceit, in my opinion.
The Clocktown Game, on the other hand, I think is really cool. You get to see all the routines and problems that characters have over those three days, and nudge events towards desired outcomes. Exploring how all their lives intersect, and how they react in the literal face of impending doom, allows for some really cool stories and moments.
It's a Clocktown game trapped in the body of a Zelda game.
I realize this. What I meant is, 'that's why it was added', rather than 'I wish that this existed.' Relying on the time slow is recognizing that the dungeon wasn't really designed around the time loop in the first place. It just doesn't feel like a very cohesive design.