He is giving way to Grady Fuson who will oversee the draft and player development sectors.
"We are transitioning to the new regimen, the new structure we have in place," said Waller.
And that is why he is in Arizona, to entrust Fuson with the information he has gleaned over the last six years.
A veteran of 18 seasons in the Padres' organization as a coach, instructor and administrator, Waller was named Director of Player Development in September of 1999.
Waller served as San Diego's Coordinator of Minor League Instruction from 1997-99. Previously, he was the organization's minor league outfield and baserunning instructor, a post he held from 1989 to 1993. In 1994, he managed Single-A Spokane, and in 1995 he served as San Diego's Major League bullpen coach. Waller began his coaching career at Spokane in 1988 after an 11-year playing career.
An outfielder who spent parts of four seasons in the Majors, Waller was drafted by St. Louis in the fourth round in 1977 after playing two years at San Diego City College. He went on to play in the Cardinals, Cubs and Astros organizations before retiring following the 1987 campaign.
Instead of looking at reassignment as a demotion, other doors are opening for him.
Admittedly, after six years as the head man in player development, Waller eyes the future with a new set of eyes.
"I have been with the Padres for a number of years," he said. "I want to be a part of a winner and winning the World Series. I believe I have some things I can add at any level."
Six years as the guy who has to tell a prospect that he must seek work somewhere else, be there for the surgery that deflates a prospect's confidence and the everyday grind that is a 24/7/365 job is taxing.
He is on the threshold of a new opportunity.
" I am being considered for a Major League opportunity," Waller confides. "That is what I am thirsting for: winning and helping this organization.
"Baseball is who I am. This is what I know."
What better man to join the staff. He has intimate knowledge of the Padres' system - one they will likely tap into over the next few years. His presence might actually signify those players getting a chance to play.
With rumors circulating on General Manager Kevin Towers, Waller is in a holding pattern for now. He is advising Fuson today and expects to meet with the Padres top brass soon to find out what his future holds.
Stability above may play a part in his thinking but Waller has been a part of San Diego baseball for over twenty years – he played at San Diego City College and went to Hoover High School.
Baseball isn't all that he knows – the Padres can easily be clumped into that catchphrase.