Naruto: Path of the Ninja 2
actually has quite a few improvements in this department. Not only does this version have way more playable characters than the last one (this release boasts more than 30 characters), but there are a few new mechanics that actually add to the game's strategy aspect.
For one, you can now pick one of your party members as Squad Leader. Each character has certain stats that will affect the rest of the squad. One person might enhance the speed of the squad, while another increases their initial health. For the most part, each character's enhancement comes with a fairly predictable detriment. For instance, Naruto as your Squad Leader will increase your team's attack power, but at the cost of defenses.
The other system that really adds some depth to the game is Ninja Tags. These are attributes you can pick up throughout the game and apply to various characters. With this system, not only can characters learn Jutsu that aren't normally in their repertoire, but they can also gain stat boosts like resistance to Fire Jutsu. Also, you have to be careful how you allot these Tags because each character has only a certain number of slots, and the more powerful the Ninja Tag, the more slots it takes up, but at least you gain more slots as your character levels up, so it tends to balance out nicely.
So what's the story for Path of the Ninja 2? Well, it takes place after Sasuke has left the village, but before Naruto leaves to train with Jiraiya, so, like many games are doing right now, it's the perfect place to put unique storylines instead of trying to stick to the TV series. Here, a band of rogue ninja are trying to wake up an ancient evil to destroy the Hidden Leaf Village. While not exactly a shocking storyline, it is fairly fun and compelling enough to work your way through the game, plus there are various points (via flashbacks and what not), where you will get to go through some of the bigger fights from the series like the fight between Sasuke and Naruto, so that's always a plus.