TP is far darker than OoT.
There are quite a few deaths in TP, many of them implied. For example, the Kakariko residents were brutally massacred by shadow beasts prior to your arrival in the town; not only do their deaths occur, but the haunting feeling of desolation throughout the town, of fatigue and despair exhuded by Renado, contribute to a feeling of hopelessness and heavy loss. It's not the number of deaths, or the fact of death, that darkens the mood, but rather the emotional and atmospheric consequences of death, and this is something that OoT lacked relative to TP; you feel little grief at the death of the Deku Tree, or of the Castle Towners (other than that initial lapse of horror upon leaving the ToT as an adult), but TP leads you to empathize with the struggles of Renado, of Ilia, of Ralis and Rutela (another tragic death far more emotional than any in OoT btw), of Colin, of Zelda, of Midna, and so many more.
Besides, TP carries far heavier and more twisted themes than OoT; concerning greed and manipulation, corruption and the descent into madness, the onset of hopelessness, sin and sacrifice, and struggle and suffering. All not very happy things.
Apologies for not having much to add to the OP.