Well it isn't rocket science. The winning formula is quite simple for the likes of the All Stars, Te Akau, Waller, Maher. While they go about doing the simple things very well the rest are wondering what secret potions they must have. When the truth is they don't have any other than a training method.
Another key tenet to these operations is they work on prevention of issues not waiting for issues to arise. They know the weak points common to all horses and apply preventative management to forestall them. Hence their ability to have their horses at peak for a long time and season after season. For example Waller uses Lasix during training (it's banned on race day) as he knows that all horses experience EIPH (Exercise Induced Pulmonary Haeomaraghing). He uses it as a preventative treatment.
If you start with young horses that are well bred and devoid of conformation problems you have a massive head start. But then apply lessons learnt over decades of training and use preventative treatment to keep the inevitable issues that elite equine athletes all experience at bay.
Yes it is an expensive approach as any owner will tell you with horses in those stables but it gets results. They also don't piss around with slow horses. Their approach is a scientific method approach and the reality is that many trainers in the industry particularly in this country do not have the ability to understand let alone implement such an approach.