I really hate stories that basically ignore the game totally. Well, not hate, but have a pet peeve for. I mean, c'mon. How hard is it for you to adhere to the physics the game has put out already? Some ideas, like Iveechan having Hitmonchans knuckles studded with multi-colored gems, is a good idea. It's never explained HOW he can use Thunder/Fire/Ice Punch. So it's a good ad-lib. But something like, say, changing a Pokemons demeanor totally(i.e making a pokemon like Machoke a coward isn't bad, but making Eevee a ruthless killer) is really annoying. Especially if the entire species is shown like that rather than just the one Pokemon.

Stories/fics that change the physical looks of a Pokemon without any sort of reason are annoying. WFM has a green-eyed(or was it blue?) Machop. It knows Water/Dragon attacks because of it. That is the reason for the different eye color. It doesn't have wings for the sake of being a winged Pokemon. It's not a flying Eevee that becomes "SUPER MEGA UNSTOPPABLEON" because you used every stone at sunrise and treated it really good, and it will furthermore NOT look like a golden Eevee with wings.

Finally, made-up Pokemon. It's just too hard to keep track of 400 Pokemon. If you don't like what you've been given, don't bother.