The anime isn't the end all story to every ninja. Roshi was seen in his time alive as the oldest jinchuriki, Han and some others barely got screen time. It's mostly about trying to give ninjas a fair kit that represents their assumed power.

Also what your seeing is the scale of marketing, people want to have a fun "1.0" experience seeing all the classic ninjas when they start. The 1.0 version of this game is long passed and your now seeing the effect that selling more powerful ninjas has had.

Alternate versions of ninjas are necessary to represent this, for instance, do you really think Kakashi as the leader of team seven who can do two chidoris could take on the third Raikage? He had a sharingan and was anbu, but he wasn't a legendary ninja. It's a game after all, the skillbreaks help to have a little more diversity in the "p2w" meta, but they do not replace the spirit of the game which is to acquire stronger ninjas.