I dunno, I still follow the philosophy that any changes to pokemon made overrule any previous incarnations and thus become the new standard. This was evidenced by the matter that breeding and the new evos and pre-evos, as well as all new pokemon, were treated as if they always existed in the remakes. To me, this means that ALL gens are their own retcon. What about references to past events, you say? I think the same events happen across all timelines, just altered to accommodate the changes made to pokemon at the time, such as Hoenn now possessing Megas. We just don't see them because it would be too complicated to update all regions every time a change is made. Also, don't take the matter I said "timelines" too seriously, since like I said before, I believe the current standards replace all previous ones. The people of Kanto didn't know about breeding when Red was journeying? They do now. All those pre-evos and evos? They're there now. Megas? Yes. Knowledge of all the other regions? Yes. Heck, it's even possible the pokemon introduced in other gens now live in Kanto as well. Yet, Red still takes on the gyms and fights TR.
What about the Zinnia speech, you might ask. I always thought that could be interpreted any way you want. It could be referring to the Hoenn as seen originally in the third gen. It could just be talking about an alternate Hoenn of any variety. It could even be talking about the real world. I would also like to note that it's not just Zinnia, but Hoopa's ring portals also reference accessing alternate realities to summon legends. Heck, we've even BEEN to alternate realities before, in terms of the Distortion World. Yes, they exist, but that has no bearing on the sequence of events whatsoever. The events themselves never changed, but the pokemon involved did, and even peoples' knowledge of pokemon. What about Fairy type, you ask? I'll say the same thing to this as I said to the second gen long ago: it's a fourth wall break
