There were 'extra' Pokémon in the form of Missingno., etc., so in that sense that wasn't by itself that far-fetched. A few of these have resemblances in G/S/C. Bill was a bit of a let-down, in a way, because despite being introduced in terms of slightly outré experiments involving altering Pokémon, etc., they generally faded out apart from that, and hence people suggesting that there might have been some experimental residues to find wouldn't be that surprising. There were somewhat related mechanisms, such as the hybridity thing using the computers, which they may have been vaguely aware of.
Pretty much every shipping in the anime qualifies as this, too. Oh yes. I went there. Do your worst.
To be fair, such things are often portrayed in the anime, or are actual themes there. More recently, many romance-themes episodes occurred due to Serena's presence, and there was a similar thing with May at times, if less so. They also added a romantic touch to OR/AS. Perhaps specific aspects of the ships, but mostly they're just observing things already present in the anime, and also saying that they like these things and they should be taken further.
That said, VineShipping was a bit weird, for instance. Perhaps in the process of shipping everything with everything, people got drunk, as the name would seem to suggest?
There were a few weird things already present in the anime, such as Ash effectively buying Sabrina's badge with a Pokémon, or a whole Gym that males could apparently not usually enter, and Ash's decision to go after the Gyms immediately when his Pikachu had problems even when presented with a simple type advantage.
While the requirements of some glitches may have been in some way symbolic about something existing in the game, usually the ones along the lines of catching every Pokemon, beating the E4 many times (which you could do, but there isn't much in-game reason for it, specifically.), and then decided that you also needed each form of this, and also to arrange them in the PC, could get a bit egregious.
