I believe that there are 2 ganons. Also, I don't necessarily think that there is a past and a future split time-line. Here is my explanation:
In OoT, Link is sent through time 7 years into the future to beat Ganon who has caused havoc all over the land of Hyrule. After the events of OoT, Zelda sends Link back into the 7 years past. Link goes back to the castle to tell Zelda of the news. She then proceeds to tell the King of Hyrule of what happened. Ganon is then sent to be sealed away by the sages, of which are still intact because Ganon has not caused Havoc to Hyrule. After he was sealed away, the future (of when Zelda sent link back 7 years and no Link was there) that we know it to lead to WW has been completely erased forever.
A short while later, Link tells Zelda that he must leave to find his friend Navi. He then leaves Hyrule. After years of peace, Ganon escapes the seal and takes over Hyrule, which then proceeds into the great flood because Link never came back to stop Ganon. I wonder why that is? Well, in MM, Link traveled through a hallway that twisted. Most people believe Link went through a parallel dimension. If that is the case, then there are two Hyrules: Hyrule A and Hyrule B (After going through the hallway). Also at this time his Triforce of Courage must of split into 8 shards during going through it. He wasn't in Hyrule A anymore. The forest he was in, in this case, must of still been part of Hyrule. Link travels in the forest after the events of MM. Who knows where he went. Though it defiantly would lead to TP because he eventually makes it back to Hyrule (Hyrule
I believe.
So, in conclusion, Hyrule B leads to TP while Hyrule A leads to WW. Thinking from a "Back to the Future" perspective, there is no possible way that a past branch in the time-line and a future branch in the time-line could exist, as something in the past can change something in the future. The hallway in MM is something that seems to be overlooked in my opinion, and could maybe be the major key between this split time-line. There are two different ganons in this case.