Miyamoto didn't say that ALttP was a direct sequel to LoZ. He said that it was the real sequel to Legend of Zelda and that AoL was a direct sequel/side story to LoZ.
ALttP is the real sequel to LoZ in the same sense that WW is the real sequel to Ocarina. AoL is a direct sequel/side story to LoZ in the same way the MM is a direct sequel/side story to Ocarina. Also AoL and MM share the same Link from the game which they are direct sequels/side stories to. Notice the pattern here?
All of the main games (LoZ, ALttP, Ocarina) have a direct sequel/side story that involves the same Link from whatever respective game they are a sequel to. LoZ has AoL as a direct sequel/side quest that has the same Link. Also ALttP has LA and Ocarina has MM. If this pattern continues then the next Zelda GC game (maybe GBA) will be a direct sequel/side story to WW and will have the same Link.
I would like to point out that if my theory is right that it probably means any Zelda games that don't fit in this pattern don't belong in the chronology. Of course this would be Ages and Four Swords and probably whatever GBA Zelda game Capcom is making unless of course it is the direct sequel/side story to WW.
With the pattern thing in mind here is another way to look at the time line:
Ocarina/Majora's--WW/?

--LoZ/AoL--?

/?

--ALttP/LA
I added the question marks between AoL and ALttP because I figure at some point in time Miyamoto will have to make a game or games explaining how Ganon was resurrected after AoL and trapped back into the Dark World. The direct sequel/side story to WW will probably explain how Hyrule is unflooded or how Link and Zelda find a new land to become Hyrule.