Depends. Are you going to sell the game?
If you want to use Naruto, or some other copyrighted anime IP, to make some sort of hobby project, then no harm done. But, if you start distributing it beyond close friends, even for free, you basically walk into illegality.
You cannot use any individual trademarked items without legal agreement, and you cannot copy the whole look-and-feel. So, even if skills/villages/etc are individually generic, putting those elements together in way that knocks off Naruto is still possible copyright infringement. It is admittedly grey, but do you have the money to fight in court?
Anyways, go with 2. You'll be more proud when it all comes together out of your own mind, rather than knocking off an existing world.