The golden Goddesses created calamity ganon.

[Yulia11]

First the triforce is not present. Zelda does not wield the Triforce of wisdom, Link does not wield courage and Ganondorf is killed off in TP. Instead we get somwthing far more powerful than Ganon or Demise, calamity ganon.
Second is the revival of Hylia worship, which is not present in TP, and Sheikha being incredibly advanced 10000 years prior compared to their TP counterpart. Hylia worship become not only common but also replaced the worship of other spirits, and seen in the horned statue, and likely those of golden Goddesses.
Third is the impossible coexistence of Rito and Zora, which come from Wind Waker. This is possibly due to divine intervention, either by Hylia or Golden Goddesses.
My theory is that the Golden Goddesses decide to punish Hyrule by turning the half dead Ganondorf into Calamity Ganon, as he has always been the puppet of the Goddess of power. With Link and Zelda no longer wielding pieces of the Triforce the other two decide to put them on Ganon and turn him into the monstrocity. Another theory is hat Hylia absorbed the triforce herself and Ganon was in turn to take her down, but she is able to bless link with her new powers. Not lots of good evidence but do comment.

 

[Jirohnagi]

The triforce is shown to be wielded by zelda in her final memories, Zelda's Awakening and the master sword when her power awakes she uses it instinctively on a guardian to kill it. whether it's a complete triforce or not is debatable but i'd say it is, mostly because the Triforce of courage and the Master sword go hand in hand and without one the other is weakened.

Ganondorf can never die as he is a part of the cycle of reincarnation created at the behest of Demise. In fact we see that Ganondorf has gained enough power to shuck the yoke of reincarnation off in order to gain more power.
Hylia worship seems to always be around in the series in one guise or another. Mostly as the goddess of time. Hylia of course is well known for that in SS.
The games set 10,000 years in the future the sheikah have no doubt advanced but they've also schismed thanks to Ganon, the Yiga more than likely helped Ganon return quicker.

They gathered guardian parts for him and more than likely created the Skull for him to own, guardian parts are littered everywhere i suspect Koga or one of his ancestors modified some for his use.

Horned statue is actually a demon trapped within the statue in his own words it was punishment from hylia for bargaining with mortals. He hasn't repented.

Divergent evolution was more than likely at work int he rito and zora species. in fact in BOTW we don't even know if Rito and zora are remotely related. The Rito look more birrdlike than ever.

Ganondorf has never been a puppet of the goddess, the triforce is a sentient thing and if touched by an impure heart will divest itself of the piece that individual most represents which is why ganondorf has the triforce of power in Twilight Princess. If anything he is in fact a joke of the goddess as a way of taunting Demise's spirit letting his incarnation gain a third of the power he so sought after once.

Ganondorf when he lost the triforce in it's entirety no doubt searched for other ways to gain power and he found it, no doubt through ancient rites he became an elemental force and unleashed chaos. which when you considered it wouldn't be to hard as his original incarnation was capable of creating his own dimension out of time and space, in fact Demise was equal to Hylia.

We see that Hylia is a living entity as well in BOTW possibly thanks to divergent history this would also explain in part how Calamity Ganon came about. No one knows what happens to the triforce when it's used after all.

 

[Moblinking5000]

Second is the revival of Hylia worship, which is not present in TP, and Sheikha being incredibly advanced 10000 years prior compared to their TP counterpart. Hylia worship become not only common but also replaced the worship of other spirits, and seen in the horned statue, and likely those of golden Goddesses.

There's not really any evidence for the revival of Hylia worship in the CT. The DT is the only branch that does(the goddess statue in AoL which looks a lot like Hylia)

Third is the impossible coexistence of Rito and Zora, which come from Wind Waker. This is possibly due to divine intervention, either by Hylia or Golden Goddesses.

Due to the biological and cultural differences between BotW Rito and TWW Rito, they are most likely different species. And I'm sorry, but ''the goddesses did it'' isn't good theorizing.

My theory is that the Golden Goddesses decide to punish Hyrule by turning the half dead Ganondorf into Calamity Ganon, as he has always been the puppet of the Goddess of power.

Ganondorf isn't anymore a puppet of Din than Link is of Farore or Zelda is of Nayru.