There are a number of problems that have faced EPD over the past few decades. Some are long term problems such as a police culture whereby some officers see themselves as elite enforcers instead of public servants. They often come from military backgrounds and have conservative and authoritarian political and social views. Many don't even live in Eugene. 
Another problem is poor training which encourages such perspectives and urges the use of force for self-protection even when there is no threat to the officer. 
A powerful police union and poorly-written contracts by administrators make it difficult for the command structure to create any meaningful changes and often lead the city administration to lose cases of arbitration with the rank and file when disciplinary action is taken. 
A new chief will need to be aware of all these issues and still figure out a way to reform the department. It's not an easy task.