Lore reasons for that:
(BOTW) Link has been weakened by his extensive wounds sustained one hundred years prior. Furthermore, the Shrine of Resurrection was (and still is) a prototype, and therefore flawed, which may have played a part in that.
(TOTK) Ganondorf used the highly concentrated Gloom being produced by his corpse to drain Link's strength, and even managed to break the Master Sword, which was literally forged by a deity.