Piplup is quite a good Pokemon, but you may have problem at the last dungeon of the main storyline. In return, you will have some easy time with the last dungeon of the second part of the story (except boss fight).
Piplup and Chimchar combo reminds me of my first go in this game (in Jap version).
The best Pokemon is Pikachu, as protagonist. It will help you beat the game quite easily with Discharge. But you can choose other Pokemon if you want some challenge.