I've been thinking a while about this, and I've stumbled upon a few, which (and I wouldn't be surprised if you do) you may already know.
The first is Gary, in R/S/Y.
During the early parts of the game, he owns a Raticate, when he hits Lavender Town, this Raticate is no longer on his Team. While some people say that he could have easily boxed it (which takes the fun out of all the conspiracy), others argue he was actually there to bury his Raticate.
He also talks about dead Pokemon, i.e "Your Pokemon doesn't look dead". It could either hint that his has died, or that he's a cruel kid who would "at least make your Pokemon faint".
Secondly, Paras and Parasect / Cubone
Ever notice those Tiny Mushrooms and Big Mushrooms? Is there a possibility that they're actually cut off Paras and Parasect, just as it was for Slowpoke's tails?
And with this, comes the idea of Cubone's mother. It could be crazy, but the real parent of Cubone is possibly Kangaskhan, and that when a Kangaskhan dies, the child can either take the skull (and become a Cubone) or grow up to be a Kangkaskhan. Some people may argue that no, wouldn't the Marowak evolve into Kangaskhan? Possibly, but it's probably too mutated because it's head was stuck in a skull so it never did.
And out of curiosity, where are all the female Professors in the game? (In SS/GG, there's only one woman who wishes to be like Professor Elm in New Bark Town) Could this be another conspiracy? Just like the conspiracy that Brock was abused by Professor Ivy (in the Anime)?
With the conspiracies that follow the Professor Ivy it comes to no surprise that the Pokemon World could be something else entirely, so with this, I present to you,
'Ash's Coma Conspiracy'--CapsLock
P.S: Please do note that I'm only having a bit of fun and that they're just that, conspiracies which are probably wrong. I do apologise if you find any of this content offensive or upsetting which was not my intention.