I'd like to know how
FS/
FSA coming after LttP is "perfect," since most of the places carried over from LttP to
FSA were "more intact" in
FSA than in LttP, where they were mostly in ruin.
In fact, I'd also like to know how LttP being the direct sequel to
OoT fixes anything as well, since Ganon somehow magically has the entire Triforce in LttP even though he still had to search for Wisdom and Courage and take them from Zelda and Link in
OoT.
The Miyamoto Timeline (
OoT-
LoZ/
AoL-LttP) seems to have only been reinforced by the most recent games. In order to show that Ganon has left the Dark World and the Triforce been reunited and used by a king (the two prerequisites that need to be fulfilled for
LoZ to take place after
OoT),
TWW has him break out of the seal and has Daphnes swoop down on the Triforce and make his wish. In order to show the return of Ganon after his deaths in
TWW/
LoZ,
FSA introduces a new Ganondorf who takes the trident and becomes the King of Darkness, and is then sealed by the maidens in a seal that looks awfully familiar... (these all being obvious prequel material for LttP, where he owns the trident, has the title of "King of Darkness," and is sealed away).
If anything, these more recent games have made sense of the gaps between the games in Miyamoto's timeline by supplying the missing elements. That
ST shows us a new Hyrule, one of the complications not fully resolved by
TWW, we know that Nintendo is taking meaningful steps to patch up the holes introduced by the games' often conflicting stories.
So, to recap, I think the more recent games have filled the following gaps in Miyamoto's timeline:
Oot-
LoZ/
AoL-LttP
TWW fits between
OoT and
LoZ and fixes the problem of Ganon being in the Dark World and the Triforce being divided among the chosen wielders.
FSA fits between
AoL and LttP and fixes the problem of Ganon being dead while offering him the trident, his traditional title in LttP, and sealing him away for LttP.
ST fits between
TWW and
LoZ and adds a new Hyrule to replace the flooded one, removing that complication from the timeline forever.
TP could possibly show Master Sword continuity with LttP, but it's difficult to say since it shows just as much discontinuity with
FSA due to the Mirror of Twilight, a strong link to that game, being "utterly destroyed" in the ending.