It's simple: Shikamaru fights his battles like a game of chess. He's planned out three, four, five, or ten moves ahead. He knows his opponent, knows all their options, and he forms strategies and counters to this.
Naruto goes into battle with a deluxe bag of tricks. He decides things on the spot, and can notice and exploit immediate weaknesses and mistakes. He's an instinctive fighter, but he's got excellent instinct. He doesn't form a game plan for his fight, but he's able to execute any ability he wants to, because he's planned out the best way to perform his tricks as individual moves.