Durability is important. If you have a player that is frequently injured. he is usually replaced by somebody a lot worse (like Zach Short) and that hurts the team. That is the reason why replacement level is used. If you don't think it's important though, you can use Wins Above Average instead. In Hall of Fame consideration, WAA might be better than WAR.
Baserunning is a small part of WAR and not really controverisial. I don't know why it would be considered overrated.