Waterloo is a smaller town with a thriving economy. Milton is a distant suburb of Toronto where people are moving because housing is cheaper than other GTA suburbs. It really depends on what sort of job you'll be seeking, where you'll be working, whether you prefer a small town vs. being part of a larger city, etc. Waterloo is less cosmopolitan, but has a rich history, plenty of character and more open areas and parks. Milton is rapidly becoming developed, but doesn't really have any character or history (like most new suburbs).