Why would he want to transfer from Ganondorf to Zant? To me it doesn't seem like Ganon is a sentient being in itself. It is the manifestation of Demise's curse, more like a force of hatred that thrives off any hatred directed at Hylians than anything else. Whoever is born, ressurects, or merges with it controls it. If Ganon is already with Ganondorf because of the ToP, why would Ganondorf give this power to Zant? And what can Zant do to remove the ToP from Ganondorf? Or are you saying Zant kills Ganondorf, obtains the ToP and control of Ganon in the process? It would have to happen after they arrive in Hyrule , and when Ganondorf is weak (such as when Link defeats him in battle.) I guess that could've happened that way. Although I think I prefer the concept of Zant enacting revenge on Ganondorf with the last of what is left of him as  more than to obtain his power. 

I would have transformed Ganondorf into Zant. He nevers take off his helmet, so you just see the little glimpse after the Lakebed Temple cutscene. So Zant is a new name to Ganondorf and he still posses Ganon. This time, he fuse his power with the Fused Shadows. That would have made Zant/Ganondorf even more powerful and terrifying, as he conquers both worlds and both sacred forces.

But Zant has a whole backstory with Midna that can't be ignored. The story would have to be changed a lot to adjust to Zant being Ganondorf. For starters, it wouldn't be so personal for Midna. Instead of a competitor for the monarchy taking over her crown, it would've just been a centuries old being. The story would just feel like a generic good vs. evil story imo if Zant was Ganondorf. I prefer it with all the tensions between characters. Again, two things that made Twilight Princess's story unique as opposed to a generic fantasy good vs. evil was Zant and Midna's conflict, and Zant and Ganondorf's changing relationship - from Zant worshipping Ganondorf/Ganon as a god to his betrayal of Ganondorf. In your scenario it is just bad guy Ganon is coming back,  heroes kill him, the end. Actually if Zant turned out to be Ganondorf, you have an even better argument for an Ocarina clone, since that is one fewer unique character TP would have. 

I addresed that. It would have been another time Ganon wanted to take the Triforce. But, despite Zant being Ganondorf or not, the story in TP is just that. The only difference is that Zant is a puppet rather than the new reincarnation. Zant take personal with Midna at the beggining, but at the end his main focus is Hyrule because of Ganondorf control.

I was just pointing an option to make Zant more important without the need to put another villian in the last scene. If we wanted another story, it should have been writed again and modify some things, like for example Midna being different, or keep his sarcasm until the end.

But Ganon is not a being in itself. It doesn't have memories, it only lives through other people's hatred. If Zant is a new reincarnation there would have to be some other explanation of how he knows about Hyrule, a source for his power, and a reason why he wants to conquer it. For example, Ganondorf didn't hate Hyrule because Ganon told him to. Ganondorf hated Hyrule because of how the Gerudo were treated and how Twinrova raised him. Because of his strong hatred and his ability to obtain the ToP Ganon manifests himself through Ganondorf. Zant would need a standalone motivation as well. If he is Ganondorf then the story would have to change to fit the backstory of Midna, and we would lose the character of Zant entirely. None of the characters, being limited in their knowledge would really care that he is Ganondorf, as they don't know who he is. The enemy is then just Ganondorf in disguise, but there is no reason for Ganondorf being there anyway. That would remove an entire level of depth to the story. As it is now, Ganondorf's reason for being there is that he is using Zant to get back to Hyrule and continue with his goals. As for  Midna, she is angry at Zant throughout the whole game, not just at the start of the game. This builds up with she being the one who strikes the final blow against him with the power of their people - the fused shadow, not Link. I don't really see how it is a problem anyway that Zant dies, and Ganondorf is revealed to be his manipulator. In fact, that is a much more interesting plot element than, "Zant is Ganondorf."  Zant worshipped Ganon, Ganon leaves him to die, Zant realizes his mistake and helps kill Ganondorf. All of that is very interesting. It makes for a better story.