The lights are on
Beware, do not play this game with the nunchuk! I'm proud to say that this game's combat is actually tolerable now, compared to previous efforts, playing closer to the tried-and-true Smash Brothers style than the utterly defunct mush that was, is, and will be Dissidia - Ergheiz was worse, but Dissidia still comes close. As an avid reader of the manga, I won't spoil the story, except to say it involves a maturing boy ninja with a demon fox sealed within him as the main character; an extremely emo rival out to kill his brother for wiping out his family; a reincarnating villain obsessed with snakes; a near-immortal with five hearts, and a slew of equally eccentric characters. Oh, did I mention a boyish puppet master who's also an expert assassin?
I remember the frustration of an older release, which used poor controls and a scattershot combat system to masquerade as complexity. Here, the fighting's been streamlined and is much simpler, and therefore, much more rewarding. In terms of story, adhering strictly to the story - which follows the Gaara rescue arc - in single player is frustrating, considering how badly a fan would love to explore the myriad possible matchups - say, Orochimaru versus Deidara, or maybe Kakuzu versus Sasori - but the game is still entertaining. Collecting money gives people something to do aside from running around and doing tiresome chores. I'm still waiting on that Sasuke/Itachi fight, and on the legendary Pein/Jiraiya showdown, though.
There hasn't been a new installment in this particular game in a while, but for what you are looking for I suggest Naruto Ultimate Ninja Storm 2. It has large scale boss style fights for both of the showdowns you listed. The newer one called "Generations" is good and has more characters, but the epicness of those fights is reduced.