I'm hazarding a guess and saying the biggest problem that doesn't let the split timeline "work in a sensible fashion" is that TWW refers to both MM and the OOT Adult ending?
Yes, that is, but you could argue that the Legend of the Fairy is more of an inter-game reference rather than a timeline reference. Like the pictures of Mario and friends in Hyrule Castle. But yes, it's a fairly big issue. My bigger problem is actually coming up with a decent *reason* for the timeline split in the first place, and explaining a split while at the same time not messing up the internal logic for time travel in OoT.
And, that would be the key to making an 'Almost Perfect Timeline,' since making splits work would simultaneously fix the problem of TWW and ALTTP existing in the same existence- for example, how is Hyrule destroyed when the Hyrule that has the same distinct landmarks (i.e. Spectacle Rock and Lake Hylia) as OOT Hyrule takes place after TWW, and if TWW takes place last... well, that doesn't make much sense, with Ganon's implications and the closeness to OOT, as well as some stuff TP implies as far as we can see.
I'm not *that* bothered about similar landmarks, as this is again more of an inter-game issue than a storyline issue. But the fact that Hyrule as we know it is flooded and gone forever, and that presumably all the entrances to the Sacred Realm are now underwater, and the fact that Ganon is DEAD and the Triforce is no longer with him anyway, and he also seemingly broke the seal well before TWW happened, so how can it still exist in ALttP... Yes, these are all big issues. Fitting ALttP after TWW seems impossible.
One of my solutions is this...
Gaiden timeline. No split, because I can't explain that, but an 'alternate reality'. A 'what if'. What if Ganon escaped and no hero was there to stop him? TWW is the answer to that 'what if'.
That's just a possible idea, anyway, doesn't really work with what Aonuma said though. Well, maybe, actually. Ah, who knows.
The rest of your post has confused me again. >.>