Major difference between Secret Harbour and Bunbury is that SH is still considered to be a suburb of Perth and in the metropolitan area whereas Bunbury is a city in its own right and a considerable distance from Perth and the metro area. Both excellent places to live - my brother and sister-in-law have a house and family in Bunbury. However you need to decide how far from Perth city you want to be or whether it matters at all - check out the following -
City of Bunbury - all the best, Jude and Ray