Sequels and third games
 

Does it ever make you wonder how the third games or sequels fit into the main series with the other games? I've wondered stuff about this for a while. I mean, it's pretty clear that Red/Blue and Ruby/Sapphire happen at the same time, and Gold/Silver and Diamond/Pearl happen at the same time three years later. But then you might ask, where do the third games fit in? I think they happen around the same time, but it'd be a little weird with everyone standing around in the same places yet some stuff changing around.

What's your take on it?

I believe that the 2 opposing versions are a person's point of view of what happened, while the third games are the true story of what happened. So Yellow -> Crystal -> Emerald -> Platinum. I don't know what to say about B/W and B/W2, they're obvious sequels, but both could happen. :I And then the remakes, apparently they have more priority over the 3rd versions.

After thinking about it for a short bit of time, my theory is that the third game in a given generation are what truly happened. There's always something added into the third game (Yellow - ability to get three starters, Crystal - ability to get Suicune at Tin Tower, Emerald - I'm actually clueless with this one, Platinum - Giratina shows up and Spear Pillar), Platinum and Yellow (indirectly) being the two that are the best of the third games to look at:

Yellow - Seeing as you start off with Pikachu and you have the ability to get all three starters without needing to trade from outside sources, the final battle versus Red in G/S/C makes perfect sense - Red is you from Yellow and you have had Pikachu, Venusaur, Blastoise, and Charizard for the longest time (these also happen to be Red's highest leveled Pokémon).

Platinum - At the top of Spear Pillar, you either battle Dialga or Palkia depending on if you had Diamond or Pearl, but they both essentially did the same thing to Sinnoh after Cyrus used the Red Chain on Dialga/Palkia. But in Platinum, Giratina steps in right before that happens and you go through the Distortion World and battle Giratina to stop the chaos. After beating the Elite Four and doing some side things in the post-game, you have the ability to catch both Dialga and Palkia at the top of Spear Pillar, unlike Diamond and Pearl where you can only catch one or the other - it just seems like Diamond/Pearl are missing the creator of space or time respectively where Platinum as them both.

So there's my take on the third game thing.

It's generally accepted that the third games happen instead of the paired versions. Caitlin makes a couple of references to the Battle Castle and Darach. Also, D/P/Pt take place sometime after the events that happened in the Lake of Rage in G/S/C/HG/SS.