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That was mostly just a callback to the original GSC. Archer's dialog in the original Gen 2 already confirmed that he resurrected Team Rocket in hopes of finding Giovanni:
"Oh? You managed to get this far? You must be quite the trainer. We intend to take over this Radio Station and announce our comeback. That should bring our boss Giovanni back from his solo training. We are going to regain our former glory. I won't allow you to interfere with our plans."
"No! Forgive me, Giovanni!"
"How could this be? Our dreams have come to naught. I wasn't up to the task after all. Like Giovanni did before me, I will disband Team Rocket here today. Farewell."
If FRLG are the true canon, then HGSS did a very poor job of acknowledging them. We already know about Archer resurrecting Team Rocket, but what about Team Rocket's operations in the Sevii Islands, from when he was planning all of that out? Why couldn't Archer (or someone else) have mentioned being defeated by a similar-looking kid down there 3 years ago? That would've, then, confirmed that HGSS were using FRLG as canon instead of the original games.
And, again, I repeat my earlier thoughts on how the Final Battle should've looked if they wanted to truly be consistent with FRLG:
One idea I remember seeing on another site in regards to Red's team was that HGSS could've taken advantage of the dual-slot mode on DS Lites and had the final battle on Mt. Silver literally be whoever your character and team in FRLG was. Not only would this have made both Red and Leaf equally canon, but it would also give them teams that are completely unbiased and consistent with FRLG.
Of course, they obviously would've still had to create a "default" team for those who didn't have FRLG or a DS Lite, which could've looked something like this:
- Togekiss
- Espeon
- Snorlax
- Articuno
- Zapdos
- Moltres
No starters, because you could only get one, and that would unfairly privilege one option over another. And, Togepi was a gift exclusive to FRLG, so having Togekiss explicitly recalls those games and not the originals. As for the birds... Well, why not? It's a final battle, so it's supposed to be tough, and those birds still have lower BSTs than Lance's Dragonite Trio.
To add onto that, I would have had the "default" Player Character be Red in HeartGold and Leaf in SoulSilver, so they're both equally acknowledged and one isn't favored over the other. Which fits in perfectly with FRLG.
Now, where ORAS fits in is interesting, I was seriously hoping it would be a sequel so that we WOULDN'T have this issue, but it looks more like a remake, however I'm going to try my best to treat it as a sequel in my mind.
Also, it's interesting to note that in B2/W2 there is a couple consisting of a former Team Magma and former Team Aqua Grunt, which suggests that the teams had been taken down by then, which means ORAS couldn't happen at the same time or after X and Y.
Unfortunately, ORAS are remakes, not sequels, so based on your earlier thoughts, they DO overwrite Emerald. Can't pick and choose. That means, for example, if Juan fails to appear in ORAS, then his existence is just as sketchy as the likes of Jessie, James, Kris, and Leaf, and the canonicity of the PWT and possibly, B2W2 themselves will be called into question.
In other words, the timeline is screwed. :dizzy:
You're always overcomplicating things. No duh we knew Archer from Gen II, but he never appeared in Gen I, but he DID appear in Gen III with FR/LG. And why does Red's team need to be so exact? His current team is 100% possible with FR/LG and it is a homage to Yellow, it doesn't mean Yellow is the canon story of Kanto, but it's to show that Red hasn't changed his team much over the years. Obviously Gen II was based on events from Yellow, but I think they wanted to keep his team with the mascots of the Gen I games and Gift/Event Pokemon Lapras and Snorlax. It just wouldn't feel right if he had Legendaries. It doesn't have to necessarily make sense 100% of the time, maybe they just want to keep Red old school, ever think about that? There could also be a nostalgia factor in the decisions to keep his team about the same.