I didn't rate Batman Begins all that highly - I think it was mostly sheer relief that caused people to praise it to the skies - but the plot was that there was an obvious villain, then a twist where there was a secret villain controlling him. So they did need two bad guys.

Whether or not they should have "wasted" Scarecrow as the decoy villain is another argument entirely, but IIRC isn't he still alive at the end of the movie and ready to escape from Arkham at the drop of a wide-brimmed hat?