He was going through a colour crisis
Yellow/gold shirt with black overalls
white shirt with black overalls
Even his size, stature and, face evolved alot in a short period of time.
Ever since his introduction he was changing and around the early 2000's is when we got the Wario we know today
Pink shoes where probably just another experiment with his design, Though i can't say why they thought it was a good idea but it works.