That's what I meant. We don't know when they truly started their work on the systems and for all we know they were just tweaking it when we met them. That means that Bebe's could have been started at least before our journeys or after, it's all up for interpretation at this point. Their work in itself doesn't really have much to do with the main events that we go through in the respective regions looking at it that way.
Gens 3 and 4 are the only ones with parallel worlds with drastic dynamic changes to the story unlike all past and current games.
Parallels to all the Initial Duo games are always even, and the first two thirds didn't change much with the main story while Gens 3 and 4 game second tellings of the stories with a heavy change to the overall plot to include both original Legends Plus one.
I'll admit that I didn't fully look at the part about the opinion thing and may have jumbled up something there and I apologise for that.
As for them making themselves noticeable, I still have to disagree and say that they did it often enough. They did harass people for items they needed(Devon Goods on a few occasions, Meteorite), Magma in Emerald really made themselves known when they had planned to take over the Space Center in Mossdeep, they made themselves known when they stole Captain Stern's sub, surely everyone didn't think their being all over Lilycove was a vacation, and the weather crisis among other things.
Whether or not their actions were as bad is arguable but they certainly did more than enough to make themselves pretty noticeable if you ask me. Like Galactic and Rocket, they did not keep nearly as secretive as Plasma. Plasma, or Ghetsis mainly rather, was giving everyone something reasonable to think about while hiding out their (Ghetsis') true intentions while Magma and Aqua had no problem at all resorting to thievery, etc. to get what they wanted like other teams.
Gen III and IV did screw up a lot with how things went, making it hard to understand what truely is canon and what isn't. As infer mentioned above, they could very well pull a Zelda timeline.
I was more referring to how Cerber had brought up about them being mentioned as 'new' types then, although that was since taken away in later games and remakes. They're constantly adding and taking things away, so it can get confusing.
Also Gamefreak could pull a Zelda Timeline on us...
Thank you for finally being someone who at least tries to look at my side on things. I'm not 100% against the idea of them happening around the time of RBYFrLg, I don't see it like that though, especially after what was brought up in the 5th gen.
It's just tiring when everyone uses the ol' 'Bulbapedia says it so it's law' argument when the site itself doesn't even have much of anything concerning the matter specifically, it's more placed the way it is based on really loose things. Trading directly also has little to do with the main plots themselves because they could just simply be retconning things. B2W2 has direct trade and battle with BW, even though they take place two years later, so that breaks any 'direct trade means they happen at the same time' mold. Pretty much it unless I've missed anything. Still early at the time of writing this.
As for the whole Zelda timeline subject, I've actually read up on people who have a similar thinking about that. They could very well pull one on us like that with Gen III and IV messing things up with drastic differences in versions.