I never really understood why the Pokemon anime was hated to death until recently. Although the anime has some faithful viewers, it should be left alone in fan fics. If your fic has one of these, then it's very likely to fail.
-Having a trainer wake up to get his/her first Pokemon from a professor
Basically, it's been over done. If you plan to use this, I pray that it has a plot that'll blow everyone away.
-Characters (especially those being too perfect) that lack personality and different traits from each other
Almost every character in the Pokemon anime has this problem. Avoid it at all costs.
-One sided battles
Try to make the tide of the battle shift every now and then.
-The hero/heroine gets too many "lucky breaks" every time he/she is about to lose
Luck is good for the hero, but every time things look grim can be annoying.
-Pokemon pulling a stunt that breaks the game's rules to win a battle (ex. never-miss moves like Swift and Magical Leaf being dodged other than by Fly or Dig, Electric attacks damaging Ground-type Pokemon, etc)
Remember all the times Pikachu's attacks could do heavy damage to Ground Pokemon? If you don't know that Ground-types are immune to Electric attacks by now, you shouldn't even bother writing a Pokemon fan fiction.
-Too much dialogue, especially in battles
Unless you're writing a script fic (which I highly recommend reading Pocket Monsters Chronicles
to get an idea of how it should be done), there's no reason for dialogue to dominate your fic. In a battle, try to describe the battle.
"Oh, no! Volbeat!" Karen said.
"Let's finish this," Jason said, "Aerial Ace, Meowth!"
Meowth used Aerial Ace on Volbeat.
"Oh, darn," Karen moaned, "I lost..."
-Same thing always happens in every chapter
The battle was not in Karen's favor. Despite two weeks of training her Volbeat, Jason's Meowth, who wore a sumg grin, had the upper hand. With a combination of Jason's stragety of surprise attacks and Meowth's speed, Karen had a strong opponent on her hands.
Jason chuckled, knowing that victory was within his reach. "Let's finish this." He pointed ahead of him. "Meowth, use your Aerial Ace attack!"
After leaping into the air, Meowth raised his paw, and three sharp claws were revealed on the cat Pokemon's descent. Before the Volbeat knew what hit him, he felt the pain of a scratch on his side. The firefly Pokemon collapsed on the ground as Meowth landed behind his fallen opponent.
"I lost," Karen said sadly.
Take a look at the anime fillers: Ash and friends meet Pokemon and trainer, Team Rocket tries to make trouble, and Ash and friends save the day. Gets boring, does it?
To avoid this, add in some character development chapters or make some other plot twists to prevent this.
-Traveling group without a major purpose (not everyone has a goal to strive for, etc.)
Again, look at the anime. In Kanto and Johto, Ash has his Gym Battles while Misty and Brock sit on the sidelines. In Hoenn, Ash has Gym Battles, and May has Contests. However, Brock and Max don't do much.
If you have a group, give everyone a role in it that would affect the plot. Perhaps give them an individual goal. Here are some examples:
-The character is lonely and needs to join a traveling group so they could see the many wonders of the world before he/she can go home.
-The character needs some place to be and the group is heading there.
-The character shares a similar goal with the group (excluding being the best Pokemon trainer/coordinator)
Whatever the case, make the group worth something.