These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: Create-A-Pokémon 11 suffered from this, with huge arguments stemming from the typing discussions.
Create-A-Pokémon was originally a one-off idea that was just speculative, but its implementation on a battle server caused it to continue and eventually gain its own forum. Within Smogon, CAP has a one-off metagame that includes OU (the most popular tier) pokemon with CAP pokemon.
CAP ASB was also a one-off game based off of the CAP Project. It, too, grew in popularity and got its own sub-forum in the local forum games forum.
Rebound was a custom ability Colossoil had that reflected status moves back at the user on the turn Colossoil switches in, most people agreeing that having it work on every turn would be broken. Come Generation 5, and we have a official ability in Magic Bounce that does the exact same thing - but on every turn, but doesn't effect status inflicting moves like Will-O-Wisp and Toxic.
Cyclohm, the fluffy cloud-donning electric dragon, turned out to later be remarkably similar in concept and noticeably similar in appearance to Mega Ampharos.
Likewise with the Mayintec inspired design and Fighting/Flying typing Tomohawk is similar to the real Pokemon Hawlucha in body build and design.
Sidetracked by the Gold Saucer: CAP ASB was created by longtime member Deck Knight to help keep the CAP forum's blood flowing. When it was finished and gained its own subforum, it became VERY popular.
It has now been moved to Circus Maximus, the forum games section of Smogon.
"Stop Having Fun" Guys: While flavor is encouraged during the CAP process, this trope is enforced to give CAP Pokemon competitive bases. However, this does cause oddities between a Pokemon's stats, moves, and appearance.