I'm not too sure about NZ but I really wouldn't lose too much sleep over where you do your training. At the end of the day, you will get a licence and have to go and build some experience and start applying for GA and regional jobs. I think airline recruiters today are less fussed about which company trained you and more interested in filling a vacancy with someone who has the prior experience to minimise their training costs to get you online. It's about money and ease of induction for big employers. Remember you are going to be one a thousand other pilots if you join a big airline. They couldn't really care about where you did your CPL as long as you have it. Obviously if you had trained at the Empire Test Pilot School on a Learjet they might be slightly more curious.
Having said that, I would go for the company that will get you through your training with the minimum stuffing about and taking your dollar for granted, a company that takes a bit of interest in your training progression and won't simply rip you off and leave you no better off the guys who ran a cheaper CPL course down the road. The best way to find who's got the goods is to talk to students and new grads who are still fresh in the training world. Shop around and go for value for money rather than reputation.
Good luck with it.
Gin.