The game is more or less a simple, linear adventure game with some light role-playing elements, but the puzzles never even flirt with Zelda-level quality or cleverness. It usually goes something like this: you find an obstacle you can't surmount, you explore or backtrack to find a Pokemon that can overcome it, and you return to the obstacle and clear it with the Pokemon's ability. For example, you'll use a Mudkip's water attack to extinguish some burning trees, or rescue a caged Pikachu by searching for a Pokemon with a powerful Cut ability to break the bars.
Instead of fighting them, you'll capture Pokemon by circling them with the stylus a set number of times. You can't let your line be broken by the Pokemon or its attacks, or everything will be reset and you'll have to start scribbling afresh. This requires you to pay careful attention to behavior and movement patterns. Additionally, you can use Pokemon you've already captured to temporarily power up your Capture Styler, allowing it to create barriers, stun Pokemon or require fewer circles. Finally, you can send out your partner Plusle or Minun to stun the enemy with a Discharge attack, which is limited by a meter you build by... circling Pokemon. Get the picture?