Is that portion of HGSS canon? Just wondering since I was thinking about how HGSS fits into Hoenn.
Moving this here because I don't want to derail the thread.
Anyway, as far as I know, there is nothing that says it isn't or can't be considerd canon. HGSS is, chronologically, set after Emerald, and the Embedded Tower sub-plot kicks off with Mr. PokÃ©mon giving you either the Red or Blue Orb, which he supposedly received from a Hoennese acquaintance of his. To our knowledge, nothing happened to those Orbs in the intervening years in order to render that an impossibility. It is a bit strange that the old Pyre couple would let him have an Orb, but stranger things have happened (e.g. a punk girl with the DNA Splicers). Oak seems to have been in possession of the Jade Orb for all of that time, for whatever reason.
I, personally, do like to think of it as canon, because the Embedded Tower's history interests me, and because, at the end, Oak actually discusses the recurring theme of Legendary PokÃ©mon being attracted to certain Orbs and Stones, and that had always struck me as odd.
I suppose that there is nothing to stop you from disregarding it, though, but then, that's usually the case with post-game events.