But with the release of the updated games (firered/ leafgreen, and heartgold/ soulsilver) we found out that generations 1 occurred around the same time as ruby and sapphire
This makes no sense. FireRed and LeafGreen are NOT gen 1 games, they are gen 3, just like Ruby and Sapphire.
In FireRed/LeafGreen, we revisit Kanto sometime in a future where Dark and Steel types are known, and Pokémon breeding is not new.
But I like to think that it's around the same time as Gen 1, what with B/W being a re-boot.
Mah point exactly
Wouldn't they all begin at the same time? Just because it says "3 years ago the Silph co was attacked..." doesn't mean that Gen 2 necessarily "happened" after Gen 1.
And if your point was that you are aware they don't all take place concurrently, then why this:
I sense you've misunderstood something somewhere.
If we assume that Cynthia is in her late 20s, she could have been the regional champion long before the events of Gen 4. Green made it that far at age 10 after all!
Which doesn't change the fact that it's just not plausible to think that Generation V takes place all the way back at the start of whatever passes for continuity among the core titles and that there's nothing to suggest that, particularly since the crux of your argument - that B/W are a reboot - is inaccurate.