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Palmer + Cynthia = Barry.
Why? All three characters have a similar body plan (long limbs, curly blonde hair, long sleeves, overcoat) and are among the toughest characters in the game. (Barry is the second strongest trainer in the whole series, other than the guys who pop up in Mossdeep when you use the E-Reader in Ruby and Sapphire (non-canon, though) and Red in HGSS; Cynthia's Pokemon have all perfect stats, EVs, and IVs, a level of power only held otherwise by Joey's Rattata in HGSS; and Palmer puts up one of the most challenging and strategic fights in the game outside of the metagame) Considering that, I'm pretty sure GameFreak was considering this and using it somewhere in the plot (Mt. Coronet, perhaps. This would be especially applicable in Platinum, where you descend into the Distortion World, which is probably a counterpart for Hell, minus the brimstone and anguished souls. I think she would've wanted to say goodbye to him, if they were mother and son, since there is a chance that they wouldn't be coming back), but something tells me this would've pissed off the parents everywhere, since Palmer is married to another woman. There would have been a media shitstorm on how Pokemon 'promotes adultery' and we would've gotten another round of the preachers and pastors hating on our favorite franchise, with 350+ 'godless beasts' to rant about. Hell, Arceus could even be called a 'false god meant to lure your children to sin'.

Also, the Team Leaders are all symbolic for a real evil person, or someone who leads a similar group:

Giovanni: Al Capone
Archie: Raymond Washington and Stanley Williams (founders of the Crips, an LA gang represented by blue)
Maxie: Founder of the Bloods, the Crips' rival gang, represented by red
Cyrus: Hitler (those speeches ring a bell? His grandfather saying he had abusive (Mileage may Vary) parents? His desire to make a new world? Look no further than the furher)
Ghetsis: Ingrid Newkirk (He wants a world where there is no pet ownership or consumption of meat, in Pokemon terms, however) and Stalin (wants absolute power)

Also, I think Munna is a direct reference to that quote from RBY for a simple reason: GameFreak was throwing the good ol' brick joke, where something would be mentioned early on, and drop back towards the end. In Toy Story 3, for example, Mrs. Potatohead uses her discarded eye to see Andy, which she lost in the beginning of the first movie. A plot point that occurred 15 years before that happened.

And, since this is a ranting thread on conspiracy theories, I think the one about Brock "Barack" thing was stupid. GameFreak isn't a bunch of psychics.

Finally, I'd like to end my rant with some extra overanyalyzations:

Regis, Weather Trio, Lati@s= Paganist Nature Gods
Manaphy, Lake Trio, Victini= Cherubim (little angels)
Palkia, Heatran, Dialga, Cresselia, Darkrai= Seraphim (high-level angels)
Arceus= God or some other Monotheistic creator deity
Giratina= Satan (backstory seems to confirm it)
Kami Trio, Legendary Birds, Legendary Beasts, Tao Trio= Polynesian, Hindu or Native American deities

Noob out.

^^
The same thing happened there as I'm conviced happened to Cynthia and Barry (who are quite likely related in some way, and considering children's media, it's pretty obvious Cynthia was going to be Barry's long lost mom; or, at least she is in my head-canon). GameFreak just wanted to avoid the parental outrage and just decided to keep any parts that would involve implying that a character is an illegitamite child away from the script as far as possible. It's quite obvious that every character who has parents as NPCs either has a single mom/dad, or married parents. Nothing else.