This is a problem for everyone so don't worry. When you are doing a battle, it is good trying to visualize how you want the battle to end first to me. Think of a scene to build the battle towards before creating each individual part. Think who you want the victor to be and how you want them to win. Was it a cheap shot? Was it a massive clash of Razor Leaves and Hydro Pump? Think of a scene a work towards that scene.
Remember to be as descriptive as possible towards those scenes. I think people tend to assume since it is a Pokemon fan fiction that it they people knows what Tri-Beam looks like. Take a spin on the moves that you think has room to be changed. People aren't going to fuss at you if you make Double Kick look seriously awesome. Have fun with the battle. Pretend that you it is animated in your head.
Also, keep the pokemon moving--not just doing attack back and forth. The anime and the video games makes it look the pokemon are standing face to face all the time and slinging attacks back in forth on a linear field. That's not the case. You need to have them alive as though they are fighting for their lives. The pokemon should have the ability to know when to dodge and the trainer shouldn't spew out ever single attack (well in dialogue).
Pokemon can do more than just attacks so remember that. They can jump, dodge, catch, etc. Make it realistic like you are watching a movie.
I hope that this helped. :D