Okay, so we can talk about games that have been covered already, correct? Or use them as leverage to support placement. That was my main concern, that because discussion was closed on one game, that mean it could not be talked about anymore. In that respect, the thread would be flawed. However, if we can talk about each and every game that comes into play, then that will work out perfectly. I'm thinking we can, therefore (obviously) I'm going to choose the second possibility.
....../--TWW
OoT
......\MM--ALttP/LA--LoZ/AoL--OoS/OoA
OoT No Longer the Seal War
Now, we know that WW broke OoT as the SW. This makes OoT's connection to ALttP pretty weak. There is now virtually no connection between OoT and ALttP, other than the fact that similar events occurred in the BS of ALttP as did in OoT. However, with WW, we know these events were NOT the same.
Having gotten that out of the way, we now also know that the Seal War had to be a separate event. When we look at ALttP's BS and in-game details, we find that the same stuff applies from SNES to GBA version (look on page 4, my post with the green highlighted portions of quotes, for details). A war broke out in Hyrule because people were frantically searching for the Triforce, or the entrance to the Sacred Realm (SR). Eventually, Ganondorf (the man, not yet the beast) found this entrance. He went in, wished on the Triforce (which did NOT split), and transformed the SR into the Dark World as well as a mirror image of Hyrule itself, all its inhabitants into evil creatures, and Ganondorf himself into the beast known as Ganon. Ganon then did not come out of the SR, as it was sealed by the Sages, and remained in there until the events of ALttP, when he ultimately died in there.
Placement of the Seal War
In order for the SW to happen at any point in time, we know at this point that it HAS to come after OoT. It also HAS to come on the CT, as Hyrule is flooded on the AT. Last, but definitely not least, we know that it HAS to occur during a time when Ganondorf was still a man. This would place it after OoT, MM, and before ALttP.
Different Events on the AT and CT
Now being that WW branches off from the events of Ganondorf's defeat and sealing, we know that on the CT, these events did not take place. Something else had to happen, which we will come to later on exactly what happened as shown in TP. How do we know that the same events did not happen? By looking at the remaining games. We know that ALttP, LoZ, AoL, and OoX all take place in Hyrule. This land was flooded and washed away forever in WW. Therefore, we know that these games have to come on the CT, and we know that Hyrule did not get flooded on this side, and ultimately that the events of the AT were not the same as the CT in the fact that Ganondorf did not succeed in taking over Hyrule on the CT.
Ganondorf's Immortality
We cannot assume that Ganondorf was able to live long enough from the events of OoT to the Seal War. He had to have some outside means of staying alive. Knowing this, and seeing that he lived for over 100 years in from OoT to WW on the AT, we can assume that he did enter the SR on the CT still, obtained the Triforce of Power, yet was not successful in taking over Hyrule. We know what happened because TP tells us, but again, at this point, we will just say he did not succeed in taking over. But my own personal theory is that he did obtain the Triforce.
My reasoning for this is Link being sent back to his time is controversial, but he was sent back while the Door of Time was open. This had to be a time when he had obtained all three stones. Keeping in mind the general beliefs of time travel, if you were looking at Child Link pull the MS out, you would see him pull the MS out, then just a short time later, you would see him return from the future. This would mean that Ganondorf would have time to enter, steal the ToP, and escape while Link was frozen in time. After he pulled the MS out, and before he returned from the future. Again, this would be the only way to explain Ganondorf being able to stay alive from OoT to the SW, since we do not know how long Gerudos live and can only assume that they live the normal length of humans (excluding Twinrova, of course).
Why LoZ/AoL Cannot Be Before ALttP
Now, there still remains the question of why LoZ can't be before ALttP. And I know people will still try to argue it. So let me give a few points to counter those arguments.
In LoZ, we see Ganon (beast mode), with possession of the ToP. Some try to say that he can change from Ganondorf to Ganon at will, as we have seen him do it in other games like OoT. However, his transformation from Ganondorf to Ganon is much different than his solid Ganon form we see in LoZ and ALttP. Nintendo themselves even knew this, as they wrote it in ALttP. ALttP clearly gave us insight into Ganondorf's history, and how he became stuck in the form of Ganon. I gave that history above, highlighted in green. Therefore, since he is in this form in LoZ, and the time that he became this form was during the SW, And the fact that he did not leave the SR from the time of the SW to ALttP, we must clearly see that ALttP is a prequel.
LoZ only states that Ganon stole the Triforce of Power. This happened in OoT for the first time. There is nothing to say that he could not have lost it, and captured it again. This is why LoZ's BS is its downfall, as it does not reference any other game in particular. The most solid piece of evidence is that Ganon is in his pig form, which I explained above why that means ALttP has to be a prequel.
In the end, you would have:
....../--TWW
OoT
......\MM--(SW)--ALttP/LA--LoZ/AoL--OoX