Warning: Crackpot theory time.
I just finished a play-through of ALttP, and a thought crossed my mind as I watched all of the people coming back to life. Please, bear with me until the end of this idea, since it may be a tad confusing and involves a couple of 'What if's.
Now if memory serves me right, we've already established, or at least speculated, that ALttP's Link wished to undo Ganon's evil ,or in other words, undo his wish. We also already know that Ganon gained the power of the Triforce in the DT by defeating OoT Link.
-What if #1: What if in the original timeline, OoT Link is actually defeated by Ganon and there is no split?
[Timeline: SS - OoT - ALttP]
Or in other words, the DT is the original timeline. So after ALttP Link defeats Ganon, and wishes to have Ganon's wish undone, his evil purged from the world. I think the only way this could be truly accomplished, is by preventing Ganon from making his wish in the first place.
-What if #2: What if by wishing to undo Ganon's wish, history is altered where OoT Link defeats Ganon and his wish for world domination is prevented.
............................WW/PH - ST
............................/
[Timeline: SS - OoT =/= ALttP/LA - FSS* - LoZ/AoL]
............................\
............................MM - TP - OoX*
Since Link defeats Ganon in OoT, the CT and AT form as they should, Ganon's evil is wiped away from the DT, which continues into the rest of the classic games.
I think this theory offers a potential solution to the mysterious third timeline, at least it satisfies my need for one anyways. I want to know what you guys think of my crackpot theory.
*This is simply my personal placement for OoX and FFS, since I feel they work best in these spots.