You actually caught me off guard with some of your arguments, too, and I thought you were really trying to hold back from decking me, haha. I'm more used to seeing the usual 'bulbapedia says so' or 'they are in same gen' and didn't fully expect someone to continue on like you did.
You brought some interesting points on top of that, like the Mr Pokemon receiving the orbs, which was tricky to counter because Gamefreak sometimes makes you wonder what's possibly canon and what is something they only brought to make certain Pokemon, etc. available in another region's games. Points like that above can make sense either way if you think about it.
I'll admit though, I thought Kanto and Hoenn's storylines had a connection way back before they really starting making time changes apparent. Once they started making more drastic differences like Emerald/Platinum and Steven's bizarre appearances and sayings in later games, that only furthered the chaos that is RSE's placement. If there really is a true timeline to come out, we may very well get some branches like the Zelda one with splits.
This brings me back to seeing how some people cleverly were able to include various spin offs, one example being how if N had defeated you and Pokemon were separated from people(one branch) then that could lead to the Mystery Dungeon games(Pokemon only world, although somewhere else). It's interesting because although they take place in a Pokemon only world they do acknowledge the existence of humans.
